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https://files.pythonhosted.org/packages/54/05/f4034c9d9d84de5c2bfd6ba1be912ff0c05f0dec67602340055c192c5361/lorax-0.94.82.tar.gz (from https://pypi.org/simple/lorax/), version: 0.94.82 2023-09-09T21:00:05,791 Found link https://files.pythonhosted.org/packages/89/0c/f6fa76d6b65282d5c4ba2b85ae8e04f439bbd492347ae289a178ee3abd38/lorax-0.94.85.tar.gz (from https://pypi.org/simple/lorax/), version: 0.94.85 2023-09-09T21:00:05,792 Found link https://files.pythonhosted.org/packages/80/b1/9fe626f399b89d7c2a062e36a4b795fe707622020ce265ddc9cd80940a5c/lorax-0.94.86.tar.gz (from https://pypi.org/simple/lorax/), version: 0.94.86 2023-09-09T21:00:05,792 Fetching project page and analyzing links: https://www.piwheels.org/simple/lorax/ 2023-09-09T21:00:05,793 Getting page https://www.piwheels.org/simple/lorax/ 2023-09-09T21:00:05,794 Found index url https://www.piwheels.org/simple/ 2023-09-09T21:00:06,079 Fetched page https://www.piwheels.org/simple/lorax/ as text/html 2023-09-09T21:00:06,083 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.93.20-py3-none-any.whl#sha256=782c49b5ab89e53b404a63c02ed085fd1b92765e5ec16b324800b825aa76bd2a (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,084 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.93.22-py3-none-any.whl#sha256=3de8c8281bee4fa1465223e7ab6ca8f772cce73046b49b9abc04e0b11ff8294a (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,085 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.93.23-py3-none-any.whl#sha256=d3da61e2d1969a811ce9c51c5aff006185d82bad25116f188ff49cf820522dd7 (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,085 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.93.24-py3-none-any.whl#sha256=63a3427bb571384be9deb50ca8abbfc3f9252be6f5963d760ca73fdf0be74c5c (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,086 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.93.25-py3-none-any.whl#sha256=16de7e548a3dd43aae5d3e0314e2f73dc5e0f179d00b6d74f9b0cb89252383ef (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,086 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.93.26-py3-none-any.whl#sha256=b712943b713b1f6f1d11b9fb8ad532e1cc5e8abebb1641b93b412fa0b60ce4bd (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,087 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.1-py3-none-any.whl#sha256=44cd52a7d5cb5a2dd93f04f06f914882bae63710cb055d89e9db31fe0feb127e (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,087 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.2-py3-none-any.whl#sha256=f1b03d00109b9106265be3f3daa97581a90ce361fdba65c444b9344e6b6e3bca (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,088 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.3-py3-none-any.whl#sha256=c72258c3a6c81fb07669b881e8b6cb1a4c186c6e62f05a1ada289e68a1671438 (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,088 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.4-py3-none-any.whl#sha256=7738a83b64316be47321cf7b01cee617106154de2451a5002d82c4b3d646b9d3 (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,089 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.5-py3-none-any.whl#sha256=37112882fc18c26472115c6c03401aeb2e2275e0aa51693ae20a9c648bb803d9 (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,090 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.6-py3-none-any.whl#sha256=748eba7c915596b87670c065e6842a61c657e8481b0734ce0a55261d2b5ae205 (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,090 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.7-py3-none-any.whl#sha256=db752532dcd285c5060be2c3e6e51738078b1985cfa9e6a3aa6573b985319e03 (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,090 Skipping link: No binaries permitted for lorax: https://www.piwheels.org/simple/lorax/lorax-0.94.8-py3-none-any.whl#sha256=ad19f28c987c7e6af45f6f435f034fd1611dc66e584adb26fe3d5f92de2dc35f (from https://www.piwheels.org/simple/lorax/) 2023-09-09T21:00:06,091 Skipping link: not a file: https://www.piwheels.org/simple/lorax/ 2023-09-09T21:00:06,091 Skipping link: not a file: https://pypi.org/simple/lorax/ 2023-09-09T21:00:06,118 Given no hashes to check 1 links for project 'lorax': discarding no candidates 2023-09-09T21:00:06,136 Collecting lorax==0.94.10 2023-09-09T21:00:06,138 Created temporary directory: /tmp/pip-unpack-d6jbwff6 2023-09-09T21:00:06,520 Downloading lorax-0.94.10.tar.gz (300 kB) 2023-09-09T21:00:06,736 Added lorax==0.94.10 from https://files.pythonhosted.org/packages/71/c6/cf8171013c3e3b0a5bf3c4ceeeefd58b3e347ed29bf31da4dfca3c503177/lorax-0.94.10.tar.gz to build tracker '/tmp/pip-build-tracker-t0o4hog5' 2023-09-09T21:00:06,738 Running setup.py (path:/tmp/pip-wheel-353ibwf0/lorax_9f00e6d022344ffa800ea486db814974/setup.py) egg_info for package lorax 2023-09-09T21:00:06,738 Created temporary directory: /tmp/pip-pip-egg-info-gb36sgg2 2023-09-09T21:00:06,739 Preparing metadata (setup.py): started 2023-09-09T21:00:06,740 Running command python setup.py egg_info 2023-09-09T21:00:07,547 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T21:00:07,548 !! 2023-09-09T21:00:07,549 ******************************************************************************** 2023-09-09T21:00:07,549 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T21:00:07,550 versions. Please use the underscore name 'description_file' instead. 2023-09-09T21:00:07,551 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T21:00:07,552 or your builds will no longer be supported. 2023-09-09T21:00:07,553 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T21:00:07,553 ******************************************************************************** 2023-09-09T21:00:07,554 !! 2023-09-09T21:00:07,555 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T21:00:07,578 /usr/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-09T21:00:07,579 !! 2023-09-09T21:00:07,580 ******************************************************************************** 2023-09-09T21:00:07,581 The license_file parameter is deprecated, use license_files instead. 2023-09-09T21:00:07,582 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-09T21:00:07,582 or your builds will no longer be supported. 2023-09-09T21:00:07,584 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T21:00:07,584 ******************************************************************************** 2023-09-09T21:00:07,585 !! 2023-09-09T21:00:07,586 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-09T21:00:07,586 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-09T21:00:07,587 !! 2023-09-09T21:00:07,588 ******************************************************************************** 2023-09-09T21:00:07,588 Requirements should be satisfied by a PEP 517 installer. 2023-09-09T21:00:07,588 If you are using pip, you can try `pip install --use-pep517`. 2023-09-09T21:00:07,589 ******************************************************************************** 2023-09-09T21:00:07,590 !! 2023-09-09T21:00:07,590 dist.fetch_build_eggs(dist.setup_requires) 2023-09-09T21:00:10,685 running egg_info 2023-09-09T21:00:10,686 creating /tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info 2023-09-09T21:00:10,714 writing /tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/PKG-INFO 2023-09-09T21:00:10,725 writing dependency_links to /tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/dependency_links.txt 2023-09-09T21:00:10,726 writing entry points to /tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/entry_points.txt 2023-09-09T21:00:10,731 writing requirements to /tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/requires.txt 2023-09-09T21:00:10,732 writing top-level names to /tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/top_level.txt 2023-09-09T21:00:10,734 writing manifest file '/tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/SOURCES.txt' 2023-09-09T21:00:10,865 listing git files failed - pretending there aren't any 2023-09-09T21:00:10,870 reading manifest file '/tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/SOURCES.txt' 2023-09-09T21:00:10,871 reading manifest template 'MANIFEST.in' 2023-09-09T21:00:10,876 warning: no files found matching '*' under directory 'lorax/instance' 2023-09-09T21:00:10,888 no previously-included directories found matching 'FastTree-lorax' 2023-09-09T21:00:10,888 no previously-included directories found matching 'lorax/test/data' 2023-09-09T21:00:10,889 no previously-included directories found matching 'lorax/test/logs' 2023-09-09T21:00:10,890 adding license file 'LICENSE.txt' 2023-09-09T21:00:10,892 writing manifest file '/tmp/pip-pip-egg-info-gb36sgg2/lorax.egg-info/SOURCES.txt' 2023-09-09T21:00:11,022 Preparing metadata (setup.py): finished with status 'done' 2023-09-09T21:00:11,026 Source in /tmp/pip-wheel-353ibwf0/lorax_9f00e6d022344ffa800ea486db814974 has version 0.94.10, which satisfies requirement lorax==0.94.10 from https://files.pythonhosted.org/packages/71/c6/cf8171013c3e3b0a5bf3c4ceeeefd58b3e347ed29bf31da4dfca3c503177/lorax-0.94.10.tar.gz 2023-09-09T21:00:11,027 Removed lorax==0.94.10 from https://files.pythonhosted.org/packages/71/c6/cf8171013c3e3b0a5bf3c4ceeeefd58b3e347ed29bf31da4dfca3c503177/lorax-0.94.10.tar.gz from build tracker '/tmp/pip-build-tracker-t0o4hog5' 2023-09-09T21:00:11,033 Created temporary directory: /tmp/pip-unpack-fht04uys 2023-09-09T21:00:11,034 Created temporary directory: /tmp/pip-unpack-5pp2_pjw 2023-09-09T21:00:11,094 Building wheels for collected packages: lorax 2023-09-09T21:00:11,098 Created temporary directory: /tmp/pip-wheel-27raumfl 2023-09-09T21:00:11,099 Building wheel for lorax (setup.py): started 2023-09-09T21:00:11,100 Destination directory: /tmp/pip-wheel-27raumfl 2023-09-09T21:00:11,101 Running command python setup.py bdist_wheel 2023-09-09T21:00:11,862 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T21:00:11,863 !! 2023-09-09T21:00:11,864 ******************************************************************************** 2023-09-09T21:00:11,865 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T21:00:11,865 versions. Please use the underscore name 'description_file' instead. 2023-09-09T21:00:11,866 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T21:00:11,867 or your builds will no longer be supported. 2023-09-09T21:00:11,868 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T21:00:11,868 ******************************************************************************** 2023-09-09T21:00:11,869 !! 2023-09-09T21:00:11,869 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T21:00:11,894 /usr/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-09T21:00:11,895 !! 2023-09-09T21:00:11,896 ******************************************************************************** 2023-09-09T21:00:11,896 The license_file parameter is deprecated, use license_files instead. 2023-09-09T21:00:11,897 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-09T21:00:11,898 or your builds will no longer be supported. 2023-09-09T21:00:11,899 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T21:00:11,899 ******************************************************************************** 2023-09-09T21:00:11,900 !! 2023-09-09T21:00:11,901 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-09T21:00:11,901 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-09T21:00:11,902 !! 2023-09-09T21:00:11,903 ******************************************************************************** 2023-09-09T21:00:11,903 Requirements should be satisfied by a PEP 517 installer. 2023-09-09T21:00:11,904 If you are using pip, you can try `pip install --use-pep517`. 2023-09-09T21:00:11,904 ******************************************************************************** 2023-09-09T21:00:11,906 !! 2023-09-09T21:00:11,906 dist.fetch_build_eggs(dist.setup_requires) 2023-09-09T21:00:12,572 running bdist_wheel 2023-09-09T21:00:12,626 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2023-09-09T21:00:12,680 running build 2023-09-09T21:00:12,681 running build_py 2023-09-09T21:00:12,681 running build_cbinary 2023-09-09T21:00:12,682 compiling FastTree v2.1.10 binary 2023-09-09T21:00:39,526 FastTree-2.1.10.c: In function ‘CreateGTR’: 2023-09-09T21:00:39,527 FastTree-2.1.10.c:9531:10: warning: ‘CreateTransitionMatrix’ accessing 3200 bytes in a region of size 640 [-Wstringop-overflow=] 2023-09-09T21:00:39,527 9531 | return(CreateTransitionMatrix(matrix,f)); 2023-09-09T21:00:39,528 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-09T21:00:39,528 FastTree-2.1.10.c:9531:10: note: referencing argument 1 of type ‘double[20][20]’ 2023-09-09T21:00:39,529 FastTree-2.1.10.c:9531:10: note: referencing argument 2 of type ‘double[20]’ 2023-09-09T21:00:39,529 FastTree-2.1.10.c:9534:22: note: in a call to function ‘CreateTransitionMatrix’ 2023-09-09T21:00:39,530 9534 | transition_matrix_t *CreateTransitionMatrix(/*IN*/double matrix[MAXCODES][MAXCODES], 2023-09-09T21:00:39,530 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-09T21:00:39,531 FastTree-2.1.10.c: In function ‘CreateGTR.part.0’: 2023-09-09T21:00:39,532 FastTree-2.1.10.c:9531:10: warning: ‘CreateTransitionMatrix’ accessing 3200 bytes in a region of size 640 [-Wstringop-overflow=] 2023-09-09T21:00:39,532 9531 | return(CreateTransitionMatrix(matrix,f)); 2023-09-09T21:00:39,533 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-09T21:00:39,533 FastTree-2.1.10.c:9531:10: note: referencing argument 1 of type ‘double[20][20]’ 2023-09-09T21:00:39,534 FastTree-2.1.10.c:9531:10: note: referencing argument 2 of type ‘double[20]’ 2023-09-09T21:00:39,535 FastTree-2.1.10.c:9534:22: note: in a call to function ‘CreateTransitionMatrix’ 2023-09-09T21:00:39,535 9534 | transition_matrix_t *CreateTransitionMatrix(/*IN*/double matrix[MAXCODES][MAXCODES], 2023-09-09T21:00:39,536 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-09T21:00:39,536 FastTree-2.1.10.c:9531:10: warning: ‘CreateTransitionMatrix’ accessing 3200 bytes in a region of size 640 [-Wstringop-overflow=] 2023-09-09T21:00:39,537 9531 | return(CreateTransitionMatrix(matrix,f)); 2023-09-09T21:00:39,537 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-09T21:00:39,538 FastTree-2.1.10.c:9531:10: note: referencing argument 1 of type ‘double[20][20]’ 2023-09-09T21:00:39,538 FastTree-2.1.10.c:9531:10: note: referencing argument 2 of type ‘double[20]’ 2023-09-09T21:00:39,539 FastTree-2.1.10.c:9534:22: note: in a call to function ‘CreateTransitionMatrix’ 2023-09-09T21:00:39,539 9534 | transition_matrix_t *CreateTransitionMatrix(/*IN*/double matrix[MAXCODES][MAXCODES], 2023-09-09T21:00:39,540 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-09T21:00:39,540 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `IncompleteGamma.part.0': 2023-09-09T21:00:39,541 FastTree-2.1.10.c:(.text+0xe0): undefined reference to `log' 2023-09-09T21:00:39,541 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xf0): undefined reference to `exp' 2023-09-09T21:00:39,542 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `LogCorrect': 2023-09-09T21:00:39,542 FastTree-2.1.10.c:(.text+0x3b4c): undefined reference to `log' 2023-09-09T21:00:39,543 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x3b64): undefined reference to `log' 2023-09-09T21:00:39,543 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `CorrectedPairDistances.part.0.constprop.0': 2023-09-09T21:00:39,544 FastTree-2.1.10.c:(.text+0x4748): undefined reference to `log' 2023-09-09T21:00:39,545 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x4778): undefined reference to `log' 2023-09-09T21:00:39,545 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x47a4): undefined reference to `log' 2023-09-09T21:00:39,546 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x47d4): more undefined references to `log' follow 2023-09-09T21:00:39,546 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `PSameVector': 2023-09-09T21:00:39,547 FastTree-2.1.10.c:(.text+0x847c): undefined reference to `exp' 2023-09-09T21:00:39,548 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x849c): undefined reference to `exp' 2023-09-09T21:00:39,548 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x84bc): undefined reference to `exp' 2023-09-09T21:00:39,549 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x84f4): undefined reference to `exp' 2023-09-09T21:00:39,550 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x8514): undefined reference to `exp' 2023-09-09T21:00:39,551 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x8534): more undefined references to `exp' follow 2023-09-09T21:00:39,552 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `PairLogLk': 2023-09-09T21:00:39,553 FastTree-2.1.10.c:(.text+0x8d78): undefined reference to `log' 2023-09-09T21:00:39,554 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `MLSiteRates': 2023-09-09T21:00:39,554 FastTree-2.1.10.c:(.text+0xa778): undefined reference to `log' 2023-09-09T21:00:39,555 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xa82c): undefined reference to `exp' 2023-09-09T21:00:39,556 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xa848): undefined reference to `exp' 2023-09-09T21:00:39,557 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xa864): undefined reference to `exp' 2023-09-09T21:00:39,558 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xa880): undefined reference to `exp' 2023-09-09T21:00:39,558 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xa89c): undefined reference to `exp' 2023-09-09T21:00:39,559 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0xa8b8): more undefined references to `exp' follow 2023-09-09T21:00:39,560 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `GammaLogLk': 2023-09-09T21:00:39,561 FastTree-2.1.10.c:(.text+0xab0c): undefined reference to `log' 2023-09-09T21:00:39,562 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xab18): undefined reference to `log' 2023-09-09T21:00:39,562 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xac18): undefined reference to `log' 2023-09-09T21:00:39,563 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xac3c): undefined reference to `log' 2023-09-09T21:00:39,564 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xaf3c): undefined reference to `exp' 2023-09-09T21:00:39,565 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xaf54): undefined reference to `exp' 2023-09-09T21:00:39,565 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xaf6c): undefined reference to `exp' 2023-09-09T21:00:39,566 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xaf98): undefined reference to `exp' 2023-09-09T21:00:39,567 /usr/bin/ld: FastTree-2.1.10.c:(.text+0xafb4): undefined reference to `exp' 2023-09-09T21:00:39,568 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0xafd0): more undefined references to `exp' follow 2023-09-09T21:00:39,568 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `GammaLogLk': 2023-09-09T21:00:39,569 FastTree-2.1.10.c:(.text+0xb00c): undefined reference to `log' 2023-09-09T21:00:39,570 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `SplitSupport': 2023-09-09T21:00:39,571 FastTree-2.1.10.c:(.text+0x123e0): undefined reference to `log' 2023-09-09T21:00:39,571 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x12410): undefined reference to `log' 2023-09-09T21:00:39,572 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x1249c): undefined reference to `log' 2023-09-09T21:00:39,573 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x124b4): undefined reference to `log' 2023-09-09T21:00:39,574 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x126b4): more undefined references to `log' follow 2023-09-09T21:00:39,575 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `InitTopHits': 2023-09-09T21:00:39,575 FastTree-2.1.10.c:(.text+0x16338): undefined reference to `sqrt' 2023-09-09T21:00:39,576 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `SetAllLeafTopHits': 2023-09-09T21:00:39,577 FastTree-2.1.10.c:(.text+0x16fa4): undefined reference to `log' 2023-09-09T21:00:39,578 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x17060): undefined reference to `sqrt' 2023-09-09T21:00:39,579 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `TopHitJoin': 2023-09-09T21:00:39,579 FastTree-2.1.10.c:(.text+0x198b0): undefined reference to `log' 2023-09-09T21:00:39,580 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x198d4): undefined reference to `log' 2023-09-09T21:00:39,581 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `FastNJ': 2023-09-09T21:00:39,582 FastTree-2.1.10.c:(.text+0x1ce10): undefined reference to `sqrt' 2023-09-09T21:00:39,583 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `pnorm': 2023-09-09T21:00:39,584 FastTree-2.1.10.c:(.text+0x1e2f0): undefined reference to `exp' 2023-09-09T21:00:39,585 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x1e33c): undefined reference to `exp' 2023-09-09T21:00:39,586 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `TreeLogLk': 2023-09-09T21:00:39,587 FastTree-2.1.10.c:(.text+0x2423c): undefined reference to `log' 2023-09-09T21:00:39,588 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24250): undefined reference to `log' 2023-09-09T21:00:39,589 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24264): undefined reference to `log' 2023-09-09T21:00:39,590 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24294): undefined reference to `log' 2023-09-09T21:00:39,591 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x242ac): undefined reference to `log' 2023-09-09T21:00:39,592 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x242c4): more undefined references to `log' follow 2023-09-09T21:00:39,593 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `SetMLRates': 2023-09-09T21:00:39,594 FastTree-2.1.10.c:(.text+0x24ae8): undefined reference to `exp' 2023-09-09T21:00:39,595 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24b08): undefined reference to `exp' 2023-09-09T21:00:39,596 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24b28): undefined reference to `exp' 2023-09-09T21:00:39,597 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24b58): undefined reference to `exp' 2023-09-09T21:00:39,598 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24b78): undefined reference to `exp' 2023-09-09T21:00:39,599 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x24b98): more undefined references to `exp' follow 2023-09-09T21:00:39,599 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `SetMLRates': 2023-09-09T21:00:39,600 FastTree-2.1.10.c:(.text+0x24c80): undefined reference to `log' 2023-09-09T21:00:39,601 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24cc4): undefined reference to `log' 2023-09-09T21:00:39,602 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24cf8): undefined reference to `log' 2023-09-09T21:00:39,603 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24d40): undefined reference to `log' 2023-09-09T21:00:39,604 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x24d70): undefined reference to `log' 2023-09-09T21:00:39,605 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x24d9c): more undefined references to `log' follow 2023-09-09T21:00:39,606 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `tred2': 2023-09-09T21:00:39,607 FastTree-2.1.10.c:(.text+0x34e04): undefined reference to `sqrt' 2023-09-09T21:00:39,607 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `pythag': 2023-09-09T21:00:39,608 FastTree-2.1.10.c:(.text+0x34e9c): undefined reference to `sqrt' 2023-09-09T21:00:39,609 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x34ea8): undefined reference to `sqrt' 2023-09-09T21:00:39,610 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `tqli': 2023-09-09T21:00:39,611 FastTree-2.1.10.c:(.text+0x35500): undefined reference to `sqrt' 2023-09-09T21:00:39,612 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x35518): undefined reference to `sqrt' 2023-09-09T21:00:39,612 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x3553c): more undefined references to `sqrt' follow 2023-09-09T21:00:39,613 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `CreateTransitionMatrix': 2023-09-09T21:00:39,614 FastTree-2.1.10.c:(.text+0x35fc8): undefined reference to `exp' 2023-09-09T21:00:39,615 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x35fd8): undefined reference to `exp' 2023-09-09T21:00:39,616 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x35fe8): undefined reference to `exp' 2023-09-09T21:00:39,617 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x35ff8): undefined reference to `exp' 2023-09-09T21:00:39,618 /usr/bin/ld: FastTree-2.1.10.c:(.text+0x36008): undefined reference to `exp' 2023-09-09T21:00:39,618 /usr/bin/ld: /tmp/ccOyXxHK.o:FastTree-2.1.10.c:(.text+0x36018): more undefined references to `exp' follow 2023-09-09T21:00:39,619 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `CreateTransitionMatrix': 2023-09-09T21:00:39,620 FastTree-2.1.10.c:(.text+0x36b94): undefined reference to `sqrt' 2023-09-09T21:00:39,621 /usr/bin/ld: /tmp/ccOyXxHK.o: in function `main': 2023-09-09T21:00:39,622 FastTree-2.1.10.c:(.text.startup+0x1094): undefined reference to `log' 2023-09-09T21:00:39,623 /usr/bin/ld: FastTree-2.1.10.c:(.text.startup+0x10bc): undefined reference to `log' 2023-09-09T21:00:39,623 /usr/bin/ld: FastTree-2.1.10.c:(.text.startup+0x2d28): undefined reference to `log' 2023-09-09T21:00:39,624 /usr/bin/ld: FastTree-2.1.10.c:(.text.startup+0x2d54): undefined reference to `log' 2023-09-09T21:00:39,625 /usr/bin/ld: FastTree-2.1.10.c:(.text.startup+0x2f3c): undefined reference to `log' 2023-09-09T21:00:39,626 collect2: error: ld returned 1 exit status 2023-09-09T21:00:39,628 Traceback (most recent call last): 2023-09-09T21:00:39,629 File "", line 2, in 2023-09-09T21:00:39,630 File "", line 34, in 2023-09-09T21:00:39,631 File "/tmp/pip-wheel-353ibwf0/lorax_9f00e6d022344ffa800ea486db814974/setup.py", line 218, in 2023-09-09T21:00:39,631 setup( 2023-09-09T21:00:39,632 File "/usr/local/lib/python3.11/dist-packages/setuptools/__init__.py", line 103, in setup 2023-09-09T21:00:39,633 return distutils.core.setup(**attrs) 2023-09-09T21:00:39,634 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-09T21:00:39,635 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 185, in setup 2023-09-09T21:00:39,636 return run_commands(dist) 2023-09-09T21:00:39,637 ^^^^^^^^^^^^^^^^^^ 2023-09-09T21:00:39,637 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands 2023-09-09T21:00:39,638 dist.run_commands() 2023-09-09T21:00:39,639 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands 2023-09-09T21:00:39,639 self.run_command(cmd) 2023-09-09T21:00:39,640 File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1001, in run_command 2023-09-09T21:00:39,641 super().run_command(command) 2023-09-09T21:00:39,641 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-09T21:00:39,642 cmd_obj.run() 2023-09-09T21:00:39,643 File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 325, in run 2023-09-09T21:00:39,643 self.run_command("build") 2023-09-09T21:00:39,644 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-09-09T21:00:39,645 self.distribution.run_command(command) 2023-09-09T21:00:39,646 File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1001, in run_command 2023-09-09T21:00:39,646 super().run_command(command) 2023-09-09T21:00:39,647 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-09T21:00:39,648 cmd_obj.run() 2023-09-09T21:00:39,648 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build.py", line 131, in run 2023-09-09T21:00:39,649 self.run_command(cmd_name) 2023-09-09T21:00:39,650 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-09-09T21:00:39,651 self.distribution.run_command(command) 2023-09-09T21:00:39,651 File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1001, in run_command 2023-09-09T21:00:39,652 super().run_command(command) 2023-09-09T21:00:39,653 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-09T21:00:39,654 cmd_obj.run() 2023-09-09T21:00:39,654 File "/tmp/pip-wheel-353ibwf0/lorax_9f00e6d022344ffa800ea486db814974/setup.py", line 166, in run 2023-09-09T21:00:39,655 self.run_command('build_cbinary') 2023-09-09T21:00:39,656 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-09-09T21:00:39,657 self.distribution.run_command(command) 2023-09-09T21:00:39,658 File "/usr/local/lib/python3.11/dist-packages/setuptools/dist.py", line 1001, in run_command 2023-09-09T21:00:39,659 super().run_command(command) 2023-09-09T21:00:39,660 File "/usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-09T21:00:39,661 cmd_obj.run() 2023-09-09T21:00:39,662 File "/tmp/pip-wheel-353ibwf0/lorax_9f00e6d022344ffa800ea486db814974/setup.py", line 101, in run 2023-09-09T21:00:39,663 raise SystemError("Unable to compile C binary.") 2023-09-09T21:00:39,664 SystemError: Unable to compile C binary. 2023-09-09T21:00:39,720 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-09T21:00:39,734 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-09T21:00:39,734 exec(compile('"'"''"'"''"'"' 2023-09-09T21:00:39,734 # This is -- a caller that pip uses to run setup.py 2023-09-09T21:00:39,734 # 2023-09-09T21:00:39,734 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-09T21:00:39,734 # import from `distutils.core` to work with newer packaging standards. 2023-09-09T21:00:39,734 # - It provides a clear error message when setuptools is not installed. 2023-09-09T21:00:39,734 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-09T21:00:39,734 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-09T21:00:39,734 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-09T21:00:39,734 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-09T21:00:39,734 import os, sys, tokenize 2023-09-09T21:00:39,734 2023-09-09T21:00:39,734 try: 2023-09-09T21:00:39,734 import setuptools 2023-09-09T21:00:39,734 except ImportError as error: 2023-09-09T21:00:39,734 print( 2023-09-09T21:00:39,734 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-09T21:00:39,734 "the build environment.", 2023-09-09T21:00:39,734 file=sys.stderr, 2023-09-09T21:00:39,734 ) 2023-09-09T21:00:39,734 sys.exit(1) 2023-09-09T21:00:39,734 2023-09-09T21:00:39,734 __file__ = %r 2023-09-09T21:00:39,734 sys.argv[0] = __file__ 2023-09-09T21:00:39,734 2023-09-09T21:00:39,734 if os.path.exists(__file__): 2023-09-09T21:00:39,734 filename = __file__ 2023-09-09T21:00:39,734 with tokenize.open(__file__) as f: 2023-09-09T21:00:39,734 setup_py_code = f.read() 2023-09-09T21:00:39,734 else: 2023-09-09T21:00:39,734 filename = "" 2023-09-09T21:00:39,734 setup_py_code = "from setuptools import setup; setup()" 2023-09-09T21:00:39,734 2023-09-09T21:00:39,734 exec(compile(setup_py_code, filename, "exec")) 2023-09-09T21:00:39,734 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-353ibwf0/lorax_9f00e6d022344ffa800ea486db814974/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-27raumfl[/] 2023-09-09T21:00:39,734 [bold magenta]cwd[/]: /tmp/pip-wheel-353ibwf0/lorax_9f00e6d022344ffa800ea486db814974/ 2023-09-09T21:00:39,735 Building wheel for lorax (setup.py): finished with status 'error' 2023-09-09T21:00:39,736 ERROR: Failed building wheel for lorax 2023-09-09T21:00:39,738 Running setup.py clean for lorax 2023-09-09T21:00:39,739 Running command python setup.py clean 2023-09-09T21:00:40,490 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-09T21:00:40,490 !! 2023-09-09T21:00:40,491 ******************************************************************************** 2023-09-09T21:00:40,492 Usage of dash-separated 'description-file' will not be supported in future 2023-09-09T21:00:40,492 versions. Please use the underscore name 'description_file' instead. 2023-09-09T21:00:40,494 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-09T21:00:40,494 or your builds will no longer be supported. 2023-09-09T21:00:40,495 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T21:00:40,496 ******************************************************************************** 2023-09-09T21:00:40,497 !! 2023-09-09T21:00:40,498 opt = self.warn_dash_deprecation(opt, section) 2023-09-09T21:00:40,522 /usr/local/lib/python3.11/dist-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg` 2023-09-09T21:00:40,522 !! 2023-09-09T21:00:40,523 ******************************************************************************** 2023-09-09T21:00:40,524 The license_file parameter is deprecated, use license_files instead. 2023-09-09T21:00:40,525 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-09-09T21:00:40,526 or your builds will no longer be supported. 2023-09-09T21:00:40,527 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-09T21:00:40,528 ******************************************************************************** 2023-09-09T21:00:40,529 !! 2023-09-09T21:00:40,530 parsed = self.parsers.get(option_name, lambda x: x)(value) 2023-09-09T21:00:40,530 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-09T21:00:40,531 !! 2023-09-09T21:00:40,531 ******************************************************************************** 2023-09-09T21:00:40,532 Requirements should be satisfied by a PEP 517 installer. 2023-09-09T21:00:40,532 If you are using pip, you can try `pip install --use-pep517`. 2023-09-09T21:00:40,533 ******************************************************************************** 2023-09-09T21:00:40,533 !! 2023-09-09T21:00:40,534 dist.fetch_build_eggs(dist.setup_requires) 2023-09-09T21:00:41,184 running clean 2023-09-09T21:00:41,237 'build/lib' does not exist -- can't clean it 2023-09-09T21:00:41,238 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-09T21:00:41,239 'build/scripts-3.11' does not exist -- can't clean it 2023-09-09T21:00:41,366 Failed to build lorax 2023-09-09T21:00:41,367 ERROR: Failed to build one or more wheels 2023-09-09T21:00:41,369 Exception information: 2023-09-09T21:00:41,369 Traceback (most recent call last): 2023-09-09T21:00:41,369 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-09T21:00:41,369 status = run_func(*args) 2023-09-09T21:00:41,369 ^^^^^^^^^^^^^^^ 2023-09-09T21:00:41,369 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-09T21:00:41,369 return func(self, options, args) 2023-09-09T21:00:41,369 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-09T21:00:41,369 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-09T21:00:41,369 raise CommandError("Failed to build one or more wheels") 2023-09-09T21:00:41,369 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-09T21:00:41,372 Removed build tracker: '/tmp/pip-build-tracker-t0o4hog5'