2024-02-12T04:05:34,135 Created temporary directory: /tmp/pip-build-tracker-p_wxuwsd 2024-02-12T04:05:34,138 Initialized build tracking at /tmp/pip-build-tracker-p_wxuwsd 2024-02-12T04:05:34,138 Created build tracker: /tmp/pip-build-tracker-p_wxuwsd 2024-02-12T04:05:34,139 Entered build tracker: /tmp/pip-build-tracker-p_wxuwsd 2024-02-12T04:05:34,140 Created temporary directory: /tmp/pip-wheel-8dk0ipjo 2024-02-12T04:05:34,150 Created temporary directory: /tmp/pip-ephem-wheel-cache-wq2114z4 2024-02-12T04:05:34,214 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-02-12T04:05:34,228 2 location(s) to search for versions of beditor: 2024-02-12T04:05:34,228 * https://pypi.org/simple/beditor/ 2024-02-12T04:05:34,228 * https://www.piwheels.org/simple/beditor/ 2024-02-12T04:05:34,229 Fetching project page and analyzing links: https://pypi.org/simple/beditor/ 2024-02-12T04:05:34,230 Getting page https://pypi.org/simple/beditor/ 2024-02-12T04:05:34,234 Found index url https://pypi.org/simple/ 2024-02-12T04:05:34,345 Fetched page https://pypi.org/simple/beditor/ as application/vnd.pypi.simple.v1+json 2024-02-12T04:05:34,348 Skipping link: No binaries permitted for beditor: https://files.pythonhosted.org/packages/b1/4c/c9c62e6cf193d1e44898ebf5c41ac29059824c3c18911fe5a46180d7158e/beditor-1.1.9-py3-none-any.whl (from https://pypi.org/simple/beditor/) 2024-02-12T04:05:34,348 Found link https://files.pythonhosted.org/packages/bd/ec/c51c17cc8fc86d666cc250144fe23979a4de5ca87d1b82623d54ab92fbb2/beditor-1.1.9.tar.gz (from https://pypi.org/simple/beditor/), version: 1.1.9 2024-02-12T04:05:34,349 Found link https://files.pythonhosted.org/packages/5d/dd/9e08b11ba214026f779f7a1c48f5715bb3c147eecbcf7b48de188ab1454d/beditor-2.0.1.tar.gz (from https://pypi.org/simple/beditor/), version: 2.0.1 2024-02-12T04:05:34,350 Fetching project page and analyzing links: https://www.piwheels.org/simple/beditor/ 2024-02-12T04:05:34,351 Getting page https://www.piwheels.org/simple/beditor/ 2024-02-12T04:05:34,353 Found index url https://www.piwheels.org/simple/ 2024-02-12T04:05:34,476 Fetched page https://www.piwheels.org/simple/beditor/ as text/html 2024-02-12T04:05:34,479 Skipping link: No binaries permitted for beditor: https://www.piwheels.org/simple/beditor/beditor-1.1.9-py3-none-any.whl#sha256=d9a7abc7ca4e098df4990ae60b741801af04b093ae9314d49221f1f1e68e27cb (from https://www.piwheels.org/simple/beditor/) 2024-02-12T04:05:34,479 Skipping link: not a file: https://www.piwheels.org/simple/beditor/ 2024-02-12T04:05:34,480 Skipping link: not a file: https://pypi.org/simple/beditor/ 2024-02-12T04:05:34,512 Given no hashes to check 1 links for project 'beditor': discarding no candidates 2024-02-12T04:05:34,543 Collecting beditor==2.0.1 2024-02-12T04:05:34,547 Created temporary directory: /tmp/pip-unpack-gn9gf_h_ 2024-02-12T04:05:34,644 Downloading beditor-2.0.1.tar.gz (276 kB) 2024-02-12T04:05:35,585 Added beditor==2.0.1 from https://files.pythonhosted.org/packages/5d/dd/9e08b11ba214026f779f7a1c48f5715bb3c147eecbcf7b48de188ab1454d/beditor-2.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-p_wxuwsd' 2024-02-12T04:05:35,590 Running setup.py (path:/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/setup.py) egg_info for package beditor 2024-02-12T04:05:35,591 Created temporary directory: /tmp/pip-pip-egg-info-363ld98r 2024-02-12T04:05:35,592 Preparing metadata (setup.py): started 2024-02-12T04:05:35,594 Running command python setup.py egg_info 2024-02-12T04:05:38,307 running egg_info 2024-02-12T04:05:38,311 creating /tmp/pip-pip-egg-info-363ld98r/beditor.egg-info 2024-02-12T04:05:38,381 writing /tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/PKG-INFO 2024-02-12T04:05:38,386 writing dependency_links to /tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/dependency_links.txt 2024-02-12T04:05:38,389 writing entry points to /tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/entry_points.txt 2024-02-12T04:05:38,394 writing requirements to /tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/requires.txt 2024-02-12T04:05:38,396 writing top-level names to /tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/top_level.txt 2024-02-12T04:05:38,399 writing manifest file '/tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/SOURCES.txt' 2024-02-12T04:05:38,614 reading manifest file '/tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/SOURCES.txt' 2024-02-12T04:05:38,617 reading manifest template 'MANIFEST.in' 2024-02-12T04:05:38,659 adding license file 'LICENSE' 2024-02-12T04:05:38,671 writing manifest file '/tmp/pip-pip-egg-info-363ld98r/beditor.egg-info/SOURCES.txt' 2024-02-12T04:05:38,844 Preparing metadata (setup.py): finished with status 'done' 2024-02-12T04:05:38,856 Source in /tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f has version 2.0.1, which satisfies requirement beditor==2.0.1 from https://files.pythonhosted.org/packages/5d/dd/9e08b11ba214026f779f7a1c48f5715bb3c147eecbcf7b48de188ab1454d/beditor-2.0.1.tar.gz 2024-02-12T04:05:38,858 Removed beditor==2.0.1 from https://files.pythonhosted.org/packages/5d/dd/9e08b11ba214026f779f7a1c48f5715bb3c147eecbcf7b48de188ab1454d/beditor-2.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-p_wxuwsd' 2024-02-12T04:05:38,869 Created temporary directory: /tmp/pip-unpack-k_9p524x 2024-02-12T04:05:38,871 Created temporary directory: /tmp/pip-unpack-zkogdz3a 2024-02-12T04:05:38,953 Building wheels for collected packages: beditor 2024-02-12T04:05:38,961 Created temporary directory: /tmp/pip-wheel-7hdxgrni 2024-02-12T04:05:38,962 Building wheel for beditor (setup.py): started 2024-02-12T04:05:38,966 Destination directory: /tmp/pip-wheel-7hdxgrni 2024-02-12T04:05:38,966 Running command python setup.py bdist_wheel 2024-02-12T04:05:41,560 running bdist_wheel 2024-02-12T04:05:41,913 running build 2024-02-12T04:05:41,913 running build_py 2024-02-12T04:05:41,988 creating build 2024-02-12T04:05:41,989 creating build/lib 2024-02-12T04:05:41,990 creating build/lib/beditor 2024-02-12T04:05:41,992 copying beditor/__init__.py -> build/lib/beditor 2024-02-12T04:05:41,995 copying beditor/run.py -> build/lib/beditor 2024-02-12T04:05:42,002 creating build/lib/beditor/lib 2024-02-12T04:05:42,004 copying beditor/lib/get_mutations.py -> build/lib/beditor/lib 2024-02-12T04:05:42,008 copying beditor/lib/__init__.py -> build/lib/beditor/lib 2024-02-12T04:05:42,011 copying beditor/lib/make_guides.py -> build/lib/beditor/lib 2024-02-12T04:05:42,016 copying beditor/lib/get_scores.py -> build/lib/beditor/lib 2024-02-12T04:05:42,021 copying beditor/lib/utils.py -> build/lib/beditor/lib 2024-02-12T04:05:42,026 copying beditor/lib/methods.py -> build/lib/beditor/lib 2024-02-12T04:05:42,030 copying beditor/lib/io.py -> build/lib/beditor/lib 2024-02-12T04:05:42,035 copying beditor/lib/viz.py -> build/lib/beditor/lib 2024-02-12T04:05:42,040 copying beditor/lib/get_specificity.py -> build/lib/beditor/lib 2024-02-12T04:05:42,045 running egg_info 2024-02-12T04:05:42,113 writing beditor.egg-info/PKG-INFO 2024-02-12T04:05:42,117 writing dependency_links to beditor.egg-info/dependency_links.txt 2024-02-12T04:05:42,121 writing entry points to beditor.egg-info/entry_points.txt 2024-02-12T04:05:42,124 writing requirements to beditor.egg-info/requires.txt 2024-02-12T04:05:42,127 writing top-level names to beditor.egg-info/top_level.txt 2024-02-12T04:05:42,204 reading manifest file 'beditor.egg-info/SOURCES.txt' 2024-02-12T04:05:42,214 reading manifest template 'MANIFEST.in' 2024-02-12T04:05:42,234 adding license file 'LICENSE' 2024-02-12T04:05:42,250 writing manifest file 'beditor.egg-info/SOURCES.txt' 2024-02-12T04:05:42,255 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'beditor.bwa' is absent from the `packages` configuration. 2024-02-12T04:05:42,256 !! 2024-02-12T04:05:42,256 ******************************************************************************** 2024-02-12T04:05:42,256 ############################ 2024-02-12T04:05:42,257 # Package would be ignored # 2024-02-12T04:05:42,257 ############################ 2024-02-12T04:05:42,257 Python recognizes 'beditor.bwa' as an importable package[^1], 2024-02-12T04:05:42,258 but it is absent from setuptools' `packages` configuration. 2024-02-12T04:05:42,258 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-12T04:05:42,259 package, please make sure that 'beditor.bwa' is explicitly added 2024-02-12T04:05:42,259 to the `packages` configuration field. 2024-02-12T04:05:42,259 Alternatively, you can also rely on setuptools' discovery methods 2024-02-12T04:05:42,260 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-12T04:05:42,260 instead of `find_packages(...)`/`find:`). 2024-02-12T04:05:42,261 You can read more about "package discovery" on setuptools documentation page: 2024-02-12T04:05:42,261 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-12T04:05:42,262 If you don't want 'beditor.bwa' to be distributed and are 2024-02-12T04:05:42,262 already explicitly excluding 'beditor.bwa' via 2024-02-12T04:05:42,262 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-12T04:05:42,262 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-12T04:05:42,263 combination with a more fine grained `package-data` configuration. 2024-02-12T04:05:42,263 You can read more about "package data files" on setuptools documentation page: 2024-02-12T04:05:42,264 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-12T04:05:42,265 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-12T04:05:42,265 even if it does not contain any `.py` files. 2024-02-12T04:05:42,265 On the other hand, currently there is no concept of package data 2024-02-12T04:05:42,266 directory, all directories are treated like packages. 2024-02-12T04:05:42,266 ******************************************************************************** 2024-02-12T04:05:42,266 !! 2024-02-12T04:05:42,267 check.warn(importable) 2024-02-12T04:05:42,267 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'beditor.bwa.bwakit' is absent from the `packages` configuration. 2024-02-12T04:05:42,267 !! 2024-02-12T04:05:42,268 ******************************************************************************** 2024-02-12T04:05:42,268 ############################ 2024-02-12T04:05:42,269 # Package would be ignored # 2024-02-12T04:05:42,269 ############################ 2024-02-12T04:05:42,269 Python recognizes 'beditor.bwa.bwakit' as an importable package[^1], 2024-02-12T04:05:42,269 but it is absent from setuptools' `packages` configuration. 2024-02-12T04:05:42,270 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-12T04:05:42,270 package, please make sure that 'beditor.bwa.bwakit' is explicitly added 2024-02-12T04:05:42,271 to the `packages` configuration field. 2024-02-12T04:05:42,271 Alternatively, you can also rely on setuptools' discovery methods 2024-02-12T04:05:42,271 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-12T04:05:42,272 instead of `find_packages(...)`/`find:`). 2024-02-12T04:05:42,272 You can read more about "package discovery" on setuptools documentation page: 2024-02-12T04:05:42,273 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-12T04:05:42,273 If you don't want 'beditor.bwa.bwakit' to be distributed and are 2024-02-12T04:05:42,274 already explicitly excluding 'beditor.bwa.bwakit' via 2024-02-12T04:05:42,274 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-12T04:05:42,274 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-12T04:05:42,275 combination with a more fine grained `package-data` configuration. 2024-02-12T04:05:42,275 You can read more about "package data files" on setuptools documentation page: 2024-02-12T04:05:42,276 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-12T04:05:42,276 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-12T04:05:42,277 even if it does not contain any `.py` files. 2024-02-12T04:05:42,277 On the other hand, currently there is no concept of package data 2024-02-12T04:05:42,277 directory, all directories are treated like packages. 2024-02-12T04:05:42,278 ******************************************************************************** 2024-02-12T04:05:42,278 !! 2024-02-12T04:05:42,278 check.warn(importable) 2024-02-12T04:05:42,279 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'beditor.data' is absent from the `packages` configuration. 2024-02-12T04:05:42,279 !! 2024-02-12T04:05:42,280 ******************************************************************************** 2024-02-12T04:05:42,280 ############################ 2024-02-12T04:05:42,280 # Package would be ignored # 2024-02-12T04:05:42,280 ############################ 2024-02-12T04:05:42,281 Python recognizes 'beditor.data' as an importable package[^1], 2024-02-12T04:05:42,281 but it is absent from setuptools' `packages` configuration. 2024-02-12T04:05:42,282 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-12T04:05:42,282 package, please make sure that 'beditor.data' is explicitly added 2024-02-12T04:05:42,282 to the `packages` configuration field. 2024-02-12T04:05:42,283 Alternatively, you can also rely on setuptools' discovery methods 2024-02-12T04:05:42,283 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-12T04:05:42,283 instead of `find_packages(...)`/`find:`). 2024-02-12T04:05:42,284 You can read more about "package discovery" on setuptools documentation page: 2024-02-12T04:05:42,284 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-12T04:05:42,285 If you don't want 'beditor.data' to be distributed and are 2024-02-12T04:05:42,285 already explicitly excluding 'beditor.data' via 2024-02-12T04:05:42,286 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-12T04:05:42,286 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-12T04:05:42,286 combination with a more fine grained `package-data` configuration. 2024-02-12T04:05:42,289 You can read more about "package data files" on setuptools documentation page: 2024-02-12T04:05:42,290 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-12T04:05:42,291 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-12T04:05:42,291 even if it does not contain any `.py` files. 2024-02-12T04:05:42,291 On the other hand, currently there is no concept of package data 2024-02-12T04:05:42,292 directory, all directories are treated like packages. 2024-02-12T04:05:42,292 ******************************************************************************** 2024-02-12T04:05:42,293 !! 2024-02-12T04:05:42,293 check.warn(importable) 2024-02-12T04:05:42,293 copying beditor/beditor.ipynb -> build/lib/beditor 2024-02-12T04:05:42,294 copying beditor/workflow.ipynb -> build/lib/beditor 2024-02-12T04:05:42,299 creating build/lib/beditor/bwa 2024-02-12T04:05:42,301 copying beditor/bwa/Makefile -> build/lib/beditor/bwa 2024-02-12T04:05:42,305 copying beditor/bwa/QSufSort.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,310 copying beditor/bwa/QSufSort.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,315 copying beditor/bwa/bamlite.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,320 copying beditor/bwa/bamlite.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,328 copying beditor/bwa/bntseq.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,333 copying beditor/bwa/bntseq.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,337 copying beditor/bwa/bwa.1 -> build/lib/beditor/bwa 2024-02-12T04:05:42,343 copying beditor/bwa/bwa.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,348 copying beditor/bwa/bwa.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,352 copying beditor/bwa/bwamem.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,360 copying beditor/bwa/bwamem.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,365 copying beditor/bwa/bwamem_extra.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,369 copying beditor/bwa/bwamem_pair.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,375 copying beditor/bwa/bwape.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,381 copying beditor/bwa/bwase.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,387 copying beditor/bwa/bwase.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,391 copying beditor/bwa/bwaseqio.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,396 copying beditor/bwa/bwashm.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,401 copying beditor/bwa/bwt.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,408 copying beditor/bwa/bwt.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,414 copying beditor/bwa/bwt_gen.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,421 copying beditor/bwa/bwt_lite.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,425 copying beditor/bwa/bwt_lite.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,429 copying beditor/bwa/bwtaln.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,434 copying beditor/bwa/bwtaln.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,438 copying beditor/bwa/bwtgap.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,443 copying beditor/bwa/bwtgap.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,447 copying beditor/bwa/bwtindex.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,452 copying beditor/bwa/bwtsw2.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,458 copying beditor/bwa/bwtsw2_aux.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,464 copying beditor/bwa/bwtsw2_chain.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,468 copying beditor/bwa/bwtsw2_core.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,473 copying beditor/bwa/bwtsw2_main.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,477 copying beditor/bwa/bwtsw2_pair.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,482 copying beditor/bwa/code_of_conduct.md -> build/lib/beditor/bwa 2024-02-12T04:05:42,485 copying beditor/bwa/example.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,489 copying beditor/bwa/fastmap.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,496 copying beditor/bwa/is.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,500 copying beditor/bwa/kbtree.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,505 copying beditor/bwa/khash.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,510 copying beditor/bwa/kopen.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,515 copying beditor/bwa/kseq.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,519 copying beditor/bwa/ksort.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,524 copying beditor/bwa/kstring.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,529 copying beditor/bwa/kstring.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,533 copying beditor/bwa/ksw.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,538 copying beditor/bwa/ksw.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,543 copying beditor/bwa/kthread.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,547 copying beditor/bwa/kvec.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,551 copying beditor/bwa/main.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,555 copying beditor/bwa/malloc_wrap.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,559 copying beditor/bwa/malloc_wrap.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,563 copying beditor/bwa/maxk.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,567 copying beditor/bwa/neon_sse.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,571 copying beditor/bwa/pemerge.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,576 copying beditor/bwa/qualfa2fq.pl -> build/lib/beditor/bwa 2024-02-12T04:05:42,580 copying beditor/bwa/rle.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,584 copying beditor/bwa/rle.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,588 copying beditor/bwa/rope.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,593 copying beditor/bwa/rope.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,597 copying beditor/bwa/scalar_sse.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,601 copying beditor/bwa/utils.c -> build/lib/beditor/bwa 2024-02-12T04:05:42,605 copying beditor/bwa/utils.h -> build/lib/beditor/bwa 2024-02-12T04:05:42,609 copying beditor/bwa/xa2multi.pl -> build/lib/beditor/bwa 2024-02-12T04:05:42,613 creating build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,615 copying beditor/bwa/bwakit/README.md -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,620 copying beditor/bwa/bwakit/bwa-postalt.js -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,625 copying beditor/bwa/bwakit/run-HLA -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,629 copying beditor/bwa/bwakit/run-bwamem -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,633 copying beditor/bwa/bwakit/run-gen-ref -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,637 copying beditor/bwa/bwakit/typeHLA-selctg.js -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,641 copying beditor/bwa/bwakit/typeHLA.js -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,646 copying beditor/bwa/bwakit/typeHLA.sh -> build/lib/beditor/bwa/bwakit 2024-02-12T04:05:42,650 creating build/lib/beditor/data 2024-02-12T04:05:42,652 copying beditor/data/methods.tsv -> build/lib/beditor/data 2024-02-12T04:05:42,661 /usr/local/lib/python3.7/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-02-12T04:05:42,662 !! 2024-02-12T04:05:42,663 ******************************************************************************** 2024-02-12T04:05:42,663 Please avoid running ``setup.py`` directly. 2024-02-12T04:05:42,663 Instead, use pypa/build, pypa/installer or other 2024-02-12T04:05:42,664 standards-based tools. 2024-02-12T04:05:42,664 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-02-12T04:05:42,665 ******************************************************************************** 2024-02-12T04:05:42,665 !! 2024-02-12T04:05:42,666 self.initialize_options() 2024-02-12T04:05:42,729 installing to build/bdist.linux-armv7l/wheel 2024-02-12T04:05:42,730 running install 2024-02-12T04:05:42,788 cd /tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa;make 2024-02-12T04:05:42,793 ['/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/kstring.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/scalar_sse.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtsw2_pair.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwamem.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtsw2.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwa.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/fastmap.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bamlite.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/kbtree.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwamem.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtsw2_main.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwt.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtsw2_chain.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwt_lite.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/neon_sse.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/kstring.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/QSufSort.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/ksw.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwa.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/ksort.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtaln.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/rle.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/rle.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwaseqio.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/is.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/maxk.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/Makefile', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/kseq.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwamem_pair.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bntseq.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwt_gen.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtindex.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/code_of_conduct.md', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwase.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/qualfa2fq.pl', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwape.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bntseq.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/kthread.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwamem_extra.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtaln.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/malloc_wrap.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/malloc_wrap.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtgap.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/pemerge.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtgap.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwashm.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/rope.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bamlite.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/khash.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwakit', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtsw2_aux.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/utils.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/kopen.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/ksw.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwtsw2_core.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/main.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/xa2multi.pl', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwt.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/example.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwt_lite.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/rope.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/kvec.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/QSufSort.h', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/utils.c', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwa.1', '/tmp/pip-wheel-8dk0ipjo/beditor_6865bef1affa4068a8c75a529dd47f4f/beditor/bwa/bwase.h'] 2024-02-12T04:05:42,843 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o 2024-02-12T04:05:45,893 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o 2024-02-12T04:05:46,493 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o 2024-02-12T04:05:46,805 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o 2024-02-12T04:05:51,560 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o 2024-02-12T04:05:54,303 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o 2024-02-12T04:05:56,743 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o 2024-02-12T04:05:59,361 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o 2024-02-12T04:06:00,138 bwamem.c: In function ‘mem_align1_core’: 2024-02-12T04:06:00,138 bwamem.c:1105:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-02-12T04:06:00,139 err_printf("* %ld chains remain after removing duplicated chains\n", regs.n); 2024-02-12T04:06:00,139 ~~^ ~~~~~~ 2024-02-12T04:06:00,139 %d 2024-02-12T04:06:16,770 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o 2024-02-12T04:06:17,102 bwamem_pair.c: In function ‘mem_pestat’: 2024-02-12T04:06:17,103 bwamem_pair.c:91:99: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-02-12T04:06:17,103 if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); 2024-02-12T04:06:17,104 ~~^ ~~~~~~~~~~ 2024-02-12T04:06:17,104 %d 2024-02-12T04:06:17,105 bwamem_pair.c:91:104: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-02-12T04:06:17,105 if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); 2024-02-12T04:06:17,105 ~~^ ~~~~~~~~~~ 2024-02-12T04:06:17,106 %d 2024-02-12T04:06:17,106 bwamem_pair.c:91:109: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-02-12T04:06:17,106 if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); 2024-02-12T04:06:17,107 ~~^ ~~~~~~~~~~ 2024-02-12T04:06:17,107 %d 2024-02-12T04:06:17,107 bwamem_pair.c:91:114: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-02-12T04:06:17,108 if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); 2024-02-12T04:06:17,108 ~~^ ~~~~~~~~~~ 2024-02-12T04:06:17,108 %d 2024-02-12T04:06:19,784 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o 2024-02-12T04:06:21,330 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o 2024-02-12T04:06:21,696 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o 2024-02-12T04:06:23,230 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o 2024-02-12T04:06:23,472 bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: 2024-02-12T04:06:23,472 bwt_gen.c:879:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] 2024-02-12T04:06:23,473 bgint_t oldInverseSa0RelativeRank = 0; 2024-02-12T04:06:23,473 ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-12T04:06:23,478 bwt_gen.c: In function ‘BWTIncMergeBwt’: 2024-02-12T04:06:23,478 bwt_gen.c:953:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] 2024-02-12T04:06:23,479 unsigned int bitsInWordMinusBitPerChar; 2024-02-12T04:06:23,479 ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-12T04:06:27,548 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o 2024-02-12T04:06:29,679 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o 2024-02-12T04:06:31,871 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o 2024-02-12T04:06:33,044 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o 2024-02-12T04:06:34,355 ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o 2024-02-12T04:06:34,369 ar: `u' modifier ignored since `D' is the default (see `U') 2024-02-12T04:06:34,475 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o 2024-02-12T04:06:35,406 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o 2024-02-12T04:06:38,354 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o 2024-02-12T04:06:39,576 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o 2024-02-12T04:06:41,448 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o 2024-02-12T04:06:42,797 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o 2024-02-12T04:06:43,728 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o 2024-02-12T04:06:48,055 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o 2024-02-12T04:06:49,532 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o 2024-02-12T04:06:50,935 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o 2024-02-12T04:06:51,502 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o 2024-02-12T04:06:59,161 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o 2024-02-12T04:06:59,771 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o 2024-02-12T04:07:05,217 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o 2024-02-12T04:07:05,852 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o 2024-02-12T04:07:07,656 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o 2024-02-12T04:07:08,011 fastmap.c: In function ‘main_fastmap’: 2024-02-12T04:07:08,012 fastmap.c:448:25: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-02-12T04:07:08,012 err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l); 2024-02-12T04:07:08,013 ~~^ ~~~~~~~~~~ 2024-02-12T04:07:08,013 %d 2024-02-12T04:07:09,885 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o 2024-02-12T04:07:11,459 gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o 2024-02-12T04:07:12,059 gcc -g -Wall -Wno-unused-function -O2 bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt 2024-02-12T04:07:12,725 running install_lib 2024-02-12T04:07:12,828 creating build/bdist.linux-armv7l 2024-02-12T04:07:12,829 creating build/bdist.linux-armv7l/wheel 2024-02-12T04:07:12,833 creating build/bdist.linux-armv7l/wheel/beditor 2024-02-12T04:07:12,836 creating build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,838 copying build/lib/beditor/lib/get_mutations.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,843 copying build/lib/beditor/lib/__init__.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,846 copying build/lib/beditor/lib/make_guides.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,851 copying build/lib/beditor/lib/get_scores.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,856 copying build/lib/beditor/lib/utils.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,862 copying build/lib/beditor/lib/methods.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,867 copying build/lib/beditor/lib/io.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,873 copying build/lib/beditor/lib/viz.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,879 copying build/lib/beditor/lib/get_specificity.py -> build/bdist.linux-armv7l/wheel/beditor/lib 2024-02-12T04:07:12,885 copying build/lib/beditor/beditor.ipynb -> build/bdist.linux-armv7l/wheel/beditor 2024-02-12T04:07:12,896 creating build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,898 copying build/lib/beditor/bwa/kstring.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,903 copying build/lib/beditor/bwa/scalar_sse.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,908 copying build/lib/beditor/bwa/bwtsw2_pair.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,913 copying build/lib/beditor/bwa/bwamem.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,921 copying build/lib/beditor/bwa/bwtsw2.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,925 copying build/lib/beditor/bwa/bwa.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,929 copying build/lib/beditor/bwa/fastmap.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,935 copying build/lib/beditor/bwa/bamlite.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,940 copying build/lib/beditor/bwa/kbtree.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,945 copying build/lib/beditor/bwa/bwamem.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,949 copying build/lib/beditor/bwa/bwtsw2_main.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,954 copying build/lib/beditor/bwa/bwt.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,959 copying build/lib/beditor/bwa/bwtsw2_chain.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,963 copying build/lib/beditor/bwa/bwt_lite.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,967 copying build/lib/beditor/bwa/neon_sse.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,971 copying build/lib/beditor/bwa/kstring.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,975 copying build/lib/beditor/bwa/QSufSort.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,979 copying build/lib/beditor/bwa/ksw.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,985 copying build/lib/beditor/bwa/bwa.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,989 copying build/lib/beditor/bwa/ksort.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,994 copying build/lib/beditor/bwa/bwtaln.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:12,999 copying build/lib/beditor/bwa/rle.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,003 copying build/lib/beditor/bwa/rle.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,007 copying build/lib/beditor/bwa/bwaseqio.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,011 copying build/lib/beditor/bwa/is.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,016 copying build/lib/beditor/bwa/maxk.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,019 copying build/lib/beditor/bwa/Makefile -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,023 copying build/lib/beditor/bwa/kseq.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,027 copying build/lib/beditor/bwa/bwamem_pair.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,032 copying build/lib/beditor/bwa/bntseq.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,037 copying build/lib/beditor/bwa/bwt_gen.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,044 copying build/lib/beditor/bwa/bwtindex.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,049 copying build/lib/beditor/bwa/code_of_conduct.md -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,052 copying build/lib/beditor/bwa/bwase.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,057 copying build/lib/beditor/bwa/qualfa2fq.pl -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,060 copying build/lib/beditor/bwa/bwape.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,066 copying build/lib/beditor/bwa/bntseq.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,069 copying build/lib/beditor/bwa/kthread.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,073 copying build/lib/beditor/bwa/bwamem_extra.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,077 copying build/lib/beditor/bwa/bwtaln.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,080 copying build/lib/beditor/bwa/malloc_wrap.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,084 copying build/lib/beditor/bwa/malloc_wrap.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,088 copying build/lib/beditor/bwa/bwtgap.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,091 copying build/lib/beditor/bwa/pemerge.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,095 copying build/lib/beditor/bwa/bwtgap.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,100 copying build/lib/beditor/bwa/bwashm.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,104 copying build/lib/beditor/bwa/rope.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,108 copying build/lib/beditor/bwa/bamlite.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,111 copying build/lib/beditor/bwa/khash.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,118 creating build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,119 copying build/lib/beditor/bwa/bwakit/typeHLA.sh -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,123 copying build/lib/beditor/bwa/bwakit/bwa-postalt.js -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,128 copying build/lib/beditor/bwa/bwakit/typeHLA.js -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,133 copying build/lib/beditor/bwa/bwakit/run-gen-ref -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,137 copying build/lib/beditor/bwa/bwakit/typeHLA-selctg.js -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,140 copying build/lib/beditor/bwa/bwakit/run-bwamem -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,145 copying build/lib/beditor/bwa/bwakit/run-HLA -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,149 copying build/lib/beditor/bwa/bwakit/README.md -> build/bdist.linux-armv7l/wheel/beditor/bwa/bwakit 2024-02-12T04:07:13,153 copying build/lib/beditor/bwa/bwtsw2_aux.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,158 copying build/lib/beditor/bwa/utils.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,162 copying build/lib/beditor/bwa/kopen.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,166 copying build/lib/beditor/bwa/ksw.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,170 copying build/lib/beditor/bwa/bwtsw2_core.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,175 copying build/lib/beditor/bwa/main.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,180 copying build/lib/beditor/bwa/xa2multi.pl -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,186 copying build/lib/beditor/bwa/bwt.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,191 copying build/lib/beditor/bwa/example.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,194 copying build/lib/beditor/bwa/bwt_lite.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,198 copying build/lib/beditor/bwa/rope.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,202 copying build/lib/beditor/bwa/kvec.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,206 copying build/lib/beditor/bwa/QSufSort.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,210 copying build/lib/beditor/bwa/utils.c -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,214 copying build/lib/beditor/bwa/bwa.1 -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,220 copying build/lib/beditor/bwa/bwase.h -> build/bdist.linux-armv7l/wheel/beditor/bwa 2024-02-12T04:07:13,224 copying build/lib/beditor/workflow.ipynb -> build/bdist.linux-armv7l/wheel/beditor 2024-02-12T04:07:13,234 copying build/lib/beditor/__init__.py -> build/bdist.linux-armv7l/wheel/beditor 2024-02-12T04:07:13,240 creating build/bdist.linux-armv7l/wheel/beditor/data 2024-02-12T04:07:13,241 copying build/lib/beditor/data/methods.tsv -> build/bdist.linux-armv7l/wheel/beditor/data 2024-02-12T04:07:13,245 copying build/lib/beditor/run.py -> build/bdist.linux-armv7l/wheel/beditor 2024-02-12T04:07:13,249 running install_egg_info 2024-02-12T04:07:13,335 Copying beditor.egg-info to build/bdist.linux-armv7l/wheel/beditor-2.0.1-py3.7.egg-info 2024-02-12T04:07:13,359 running install_scripts 2024-02-12T04:07:13,417 creating build/bdist.linux-armv7l/wheel/beditor-2.0.1.dist-info/WHEEL 2024-02-12T04:07:13,423 creating '/tmp/pip-wheel-7hdxgrni/beditor-2.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-02-12T04:07:13,428 adding 'beditor/__init__.py' 2024-02-12T04:07:13,439 adding 'beditor/beditor.ipynb' 2024-02-12T04:07:13,444 adding 'beditor/run.py' 2024-02-12T04:07:13,454 adding 'beditor/workflow.ipynb' 2024-02-12T04:07:13,461 adding 'beditor/bwa/Makefile' 2024-02-12T04:07:13,466 adding 'beditor/bwa/QSufSort.c' 2024-02-12T04:07:13,469 adding 'beditor/bwa/QSufSort.h' 2024-02-12T04:07:13,472 adding 'beditor/bwa/bamlite.c' 2024-02-12T04:07:13,475 adding 'beditor/bwa/bamlite.h' 2024-02-12T04:07:13,480 adding 'beditor/bwa/bntseq.c' 2024-02-12T04:07:13,484 adding 'beditor/bwa/bntseq.h' 2024-02-12T04:07:13,494 adding 'beditor/bwa/bwa.1' 2024-02-12T04:07:13,500 adding 'beditor/bwa/bwa.c' 2024-02-12T04:07:13,503 adding 'beditor/bwa/bwa.h' 2024-02-12T04:07:13,520 adding 'beditor/bwa/bwamem.c' 2024-02-12T04:07:13,525 adding 'beditor/bwa/bwamem.h' 2024-02-12T04:07:13,529 adding 'beditor/bwa/bwamem_extra.c' 2024-02-12T04:07:13,535 adding 'beditor/bwa/bwamem_pair.c' 2024-02-12T04:07:13,545 adding 'beditor/bwa/bwape.c' 2024-02-12T04:07:13,552 adding 'beditor/bwa/bwase.c' 2024-02-12T04:07:13,555 adding 'beditor/bwa/bwase.h' 2024-02-12T04:07:13,559 adding 'beditor/bwa/bwaseqio.c' 2024-02-12T04:07:13,562 adding 'beditor/bwa/bwashm.c' 2024-02-12T04:07:13,568 adding 'beditor/bwa/bwt.c' 2024-02-12T04:07:13,571 adding 'beditor/bwa/bwt.h' 2024-02-12T04:07:13,585 adding 'beditor/bwa/bwt_gen.c' 2024-02-12T04:07:13,589 adding 'beditor/bwa/bwt_lite.c' 2024-02-12T04:07:13,591 adding 'beditor/bwa/bwt_lite.h' 2024-02-12T04:07:13,596 adding 'beditor/bwa/bwtaln.c' 2024-02-12T04:07:13,599 adding 'beditor/bwa/bwtaln.h' 2024-02-12T04:07:13,603 adding 'beditor/bwa/bwtgap.c' 2024-02-12T04:07:13,606 adding 'beditor/bwa/bwtgap.h' 2024-02-12T04:07:13,610 adding 'beditor/bwa/bwtindex.c' 2024-02-12T04:07:13,613 adding 'beditor/bwa/bwtsw2.h' 2024-02-12T04:07:13,621 adding 'beditor/bwa/bwtsw2_aux.c' 2024-02-12T04:07:13,625 adding 'beditor/bwa/bwtsw2_chain.c' 2024-02-12T04:07:13,632 adding 'beditor/bwa/bwtsw2_core.c' 2024-02-12T04:07:13,635 adding 'beditor/bwa/bwtsw2_main.c' 2024-02-12T04:07:13,640 adding 'beditor/bwa/bwtsw2_pair.c' 2024-02-12T04:07:13,643 adding 'beditor/bwa/code_of_conduct.md' 2024-02-12T04:07:13,645 adding 'beditor/bwa/example.c' 2024-02-12T04:07:13,652 adding 'beditor/bwa/fastmap.c' 2024-02-12T04:07:13,656 adding 'beditor/bwa/is.c' 2024-02-12T04:07:13,661 adding 'beditor/bwa/kbtree.h' 2024-02-12T04:07:13,667 adding 'beditor/bwa/khash.h' 2024-02-12T04:07:13,672 adding 'beditor/bwa/kopen.c' 2024-02-12T04:07:13,676 adding 'beditor/bwa/kseq.h' 2024-02-12T04:07:13,680 adding 'beditor/bwa/ksort.h' 2024-02-12T04:07:13,683 adding 'beditor/bwa/kstring.c' 2024-02-12T04:07:13,686 adding 'beditor/bwa/kstring.h' 2024-02-12T04:07:13,694 adding 'beditor/bwa/ksw.c' 2024-02-12T04:07:13,698 adding 'beditor/bwa/ksw.h' 2024-02-12T04:07:13,701 adding 'beditor/bwa/kthread.c' 2024-02-12T04:07:13,704 adding 'beditor/bwa/kvec.h' 2024-02-12T04:07:13,707 adding 'beditor/bwa/main.c' 2024-02-12T04:07:13,710 adding 'beditor/bwa/malloc_wrap.c' 2024-02-12T04:07:13,713 adding 'beditor/bwa/malloc_wrap.h' 2024-02-12T04:07:13,715 adding 'beditor/bwa/maxk.c' 2024-02-12T04:07:13,718 adding 'beditor/bwa/neon_sse.h' 2024-02-12T04:07:13,722 adding 'beditor/bwa/pemerge.c' 2024-02-12T04:07:13,725 adding 'beditor/bwa/qualfa2fq.pl' 2024-02-12T04:07:13,728 adding 'beditor/bwa/rle.c' 2024-02-12T04:07:13,731 adding 'beditor/bwa/rle.h' 2024-02-12T04:07:13,735 adding 'beditor/bwa/rope.c' 2024-02-12T04:07:13,738 adding 'beditor/bwa/rope.h' 2024-02-12T04:07:13,741 adding 'beditor/bwa/scalar_sse.h' 2024-02-12T04:07:13,744 adding 'beditor/bwa/utils.c' 2024-02-12T04:07:13,747 adding 'beditor/bwa/utils.h' 2024-02-12T04:07:13,750 adding 'beditor/bwa/xa2multi.pl' 2024-02-12T04:07:13,755 adding 'beditor/bwa/bwakit/README.md' 2024-02-12T04:07:13,762 adding 'beditor/bwa/bwakit/bwa-postalt.js' 2024-02-12T04:07:13,765 adding 'beditor/bwa/bwakit/run-HLA' 2024-02-12T04:07:13,768 adding 'beditor/bwa/bwakit/run-bwamem' 2024-02-12T04:07:13,771 adding 'beditor/bwa/bwakit/run-gen-ref' 2024-02-12T04:07:13,773 adding 'beditor/bwa/bwakit/typeHLA-selctg.js' 2024-02-12T04:07:13,779 adding 'beditor/bwa/bwakit/typeHLA.js' 2024-02-12T04:07:13,782 adding 'beditor/bwa/bwakit/typeHLA.sh' 2024-02-12T04:07:13,786 adding 'beditor/data/methods.tsv' 2024-02-12T04:07:13,789 adding 'beditor/lib/__init__.py' 2024-02-12T04:07:13,793 adding 'beditor/lib/get_mutations.py' 2024-02-12T04:07:13,798 adding 'beditor/lib/get_scores.py' 2024-02-12T04:07:13,806 adding 'beditor/lib/get_specificity.py' 2024-02-12T04:07:13,814 adding 'beditor/lib/io.py' 2024-02-12T04:07:13,820 adding 'beditor/lib/make_guides.py' 2024-02-12T04:07:13,824 adding 'beditor/lib/methods.py' 2024-02-12T04:07:13,832 adding 'beditor/lib/utils.py' 2024-02-12T04:07:13,838 adding 'beditor/lib/viz.py' 2024-02-12T04:07:13,855 adding 'beditor-2.0.1.dist-info/LICENSE' 2024-02-12T04:07:13,858 adding 'beditor-2.0.1.dist-info/METADATA' 2024-02-12T04:07:13,859 adding 'beditor-2.0.1.dist-info/WHEEL' 2024-02-12T04:07:13,862 adding 'beditor-2.0.1.dist-info/entry_points.txt' 2024-02-12T04:07:13,864 adding 'beditor-2.0.1.dist-info/top_level.txt' 2024-02-12T04:07:13,868 adding 'beditor-2.0.1.dist-info/RECORD' 2024-02-12T04:07:13,884 removing build/bdist.linux-armv7l/wheel 2024-02-12T04:07:14,124 Building wheel for beditor (setup.py): finished with status 'done' 2024-02-12T04:07:14,142 Created wheel for beditor: filename=beditor-2.0.1-py3-none-any.whl size=302510 sha256=5eeeed8e478f2cf108982e0e00bdfb8aeffbd149687317560a92a8420d5df1b2 2024-02-12T04:07:14,144 Stored in directory: /tmp/pip-ephem-wheel-cache-wq2114z4/wheels/68/38/b3/e10a4c9cf833edd39e7c5456aa56d8a917e930c453e5de28b8 2024-02-12T04:07:14,181 Successfully built beditor 2024-02-12T04:07:14,218 Removed build tracker: '/tmp/pip-build-tracker-p_wxuwsd'