2024-06-25T15:24:31,543 Created temporary directory: /tmp/pip-build-tracker-2r7pq12y 2024-06-25T15:24:31,544 Initialized build tracking at /tmp/pip-build-tracker-2r7pq12y 2024-06-25T15:24:31,544 Created build tracker: /tmp/pip-build-tracker-2r7pq12y 2024-06-25T15:24:31,545 Entered build tracker: /tmp/pip-build-tracker-2r7pq12y 2024-06-25T15:24:31,546 Created temporary directory: /tmp/pip-wheel-j23t1tay 2024-06-25T15:24:31,549 Created temporary directory: /tmp/pip-ephem-wheel-cache-ghjpph4w 2024-06-25T15:24:31,574 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-25T15:24:31,577 2 location(s) to search for versions of ont-spectre: 2024-06-25T15:24:31,577 * https://pypi.org/simple/ont-spectre/ 2024-06-25T15:24:31,577 * https://www.piwheels.org/simple/ont-spectre/ 2024-06-25T15:24:31,578 Fetching project page and analyzing links: https://pypi.org/simple/ont-spectre/ 2024-06-25T15:24:31,579 Getting page https://pypi.org/simple/ont-spectre/ 2024-06-25T15:24:31,580 Found index url https://pypi.org/simple/ 2024-06-25T15:24:31,790 Fetched page https://pypi.org/simple/ont-spectre/ as application/vnd.pypi.simple.v1+json 2024-06-25T15:24:31,792 Found link https://files.pythonhosted.org/packages/8c/ac/f5d215a7de78360886138cac41885b9b109419966ec8a9e6ffeb26c08391/ont-spectre-0.2.0.tar.gz (from https://pypi.org/simple/ont-spectre/), version: 0.2.0 2024-06-25T15:24:31,792 Found link https://files.pythonhosted.org/packages/c1/f1/1629482a61c0ee61f830cbcd418e0660c4fd2bbf3c4ba5584e3476ee0bf6/ont_spectre-0.2.1.tar.gz (from https://pypi.org/simple/ont-spectre/), version: 0.2.1 2024-06-25T15:24:31,793 Found link https://files.pythonhosted.org/packages/77/f0/48fb32bd5b1307b5dbeb8c4b514fdc725dff0e3ccf946a4af58d1b7b06fa/ont_spectre-0.2.2.tar.gz (from https://pypi.org/simple/ont-spectre/), version: 0.2.2 2024-06-25T15:24:31,794 Fetching project page and analyzing links: https://www.piwheels.org/simple/ont-spectre/ 2024-06-25T15:24:31,795 Getting page https://www.piwheels.org/simple/ont-spectre/ 2024-06-25T15:24:31,796 Found index url https://www.piwheels.org/simple/ 2024-06-25T15:24:31,960 Fetched page https://www.piwheels.org/simple/ont-spectre/ as text/html 2024-06-25T15:24:31,961 Skipping link: No binaries permitted for ont-spectre: https://www.piwheels.org/simple/ont-spectre/ont_spectre-0.2.1-py3-none-any.whl#sha256=a7f8610fcbbed8148b3c869c141ba7400ba551fb08b1634b12a9d0e611c2e252 (from https://www.piwheels.org/simple/ont-spectre/) 2024-06-25T15:24:31,962 Skipping link: No binaries permitted for ont-spectre: https://www.piwheels.org/simple/ont-spectre/ont_spectre-0.2.0-py3-none-any.whl#sha256=d0ee20985f63f04aeadc55e4657c01a6e65d21eee01ff8ac84abb42bebd14141 (from https://www.piwheels.org/simple/ont-spectre/) 2024-06-25T15:24:31,963 Skipping link: not a file: https://www.piwheels.org/simple/ont-spectre/ 2024-06-25T15:24:31,964 Skipping link: not a file: https://pypi.org/simple/ont-spectre/ 2024-06-25T15:24:31,984 Given no hashes to check 1 links for project 'ont-spectre': discarding no candidates 2024-06-25T15:24:32,003 Collecting ont-spectre==0.2.2 2024-06-25T15:24:32,006 Created temporary directory: /tmp/pip-unpack-71apn_08 2024-06-25T15:24:32,226 Downloading ont_spectre-0.2.2.tar.gz (89 kB) 2024-06-25T15:24:32,367 Added ont-spectre==0.2.2 from https://files.pythonhosted.org/packages/77/f0/48fb32bd5b1307b5dbeb8c4b514fdc725dff0e3ccf946a4af58d1b7b06fa/ont_spectre-0.2.2.tar.gz to build tracker '/tmp/pip-build-tracker-2r7pq12y' 2024-06-25T15:24:32,370 Running setup.py (path:/tmp/pip-wheel-j23t1tay/ont-spectre_e075047e9a3a4ff09bc372c6c3781382/setup.py) egg_info for package ont-spectre 2024-06-25T15:24:32,371 Created temporary directory: /tmp/pip-pip-egg-info-1fivdxq7 2024-06-25T15:24:32,371 Preparing metadata (setup.py): started 2024-06-25T15:24:32,373 Running command python setup.py egg_info 2024-06-25T15:24:32,908 /tmp/pip-wheel-j23t1tay/ont-spectre_e075047e9a3a4ff09bc372c6c3781382/setup.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-06-25T15:24:32,908 import pkg_resources 2024-06-25T15:24:33,532 running egg_info 2024-06-25T15:24:33,533 creating /tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info 2024-06-25T15:24:33,561 writing /tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/PKG-INFO 2024-06-25T15:24:33,564 writing dependency_links to /tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/dependency_links.txt 2024-06-25T15:24:33,566 writing entry points to /tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/entry_points.txt 2024-06-25T15:24:33,567 writing requirements to /tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/requires.txt 2024-06-25T15:24:33,568 writing top-level names to /tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/top_level.txt 2024-06-25T15:24:33,569 writing manifest file '/tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/SOURCES.txt' 2024-06-25T15:24:33,662 reading manifest file '/tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/SOURCES.txt' 2024-06-25T15:24:33,664 reading manifest template 'MANIFEST.in' 2024-06-25T15:24:33,665 adding license file 'LICENSE.md' 2024-06-25T15:24:33,667 writing manifest file '/tmp/pip-pip-egg-info-1fivdxq7/ont_spectre.egg-info/SOURCES.txt' 2024-06-25T15:24:33,789 Preparing metadata (setup.py): finished with status 'done' 2024-06-25T15:24:33,793 Source in /tmp/pip-wheel-j23t1tay/ont-spectre_e075047e9a3a4ff09bc372c6c3781382 has version 0.2.2, which satisfies requirement ont-spectre==0.2.2 from https://files.pythonhosted.org/packages/77/f0/48fb32bd5b1307b5dbeb8c4b514fdc725dff0e3ccf946a4af58d1b7b06fa/ont_spectre-0.2.2.tar.gz 2024-06-25T15:24:33,794 Removed ont-spectre==0.2.2 from https://files.pythonhosted.org/packages/77/f0/48fb32bd5b1307b5dbeb8c4b514fdc725dff0e3ccf946a4af58d1b7b06fa/ont_spectre-0.2.2.tar.gz from build tracker '/tmp/pip-build-tracker-2r7pq12y' 2024-06-25T15:24:33,798 Created temporary directory: /tmp/pip-unpack-4kjakpvr 2024-06-25T15:24:33,799 Created temporary directory: /tmp/pip-unpack-p7__oyt5 2024-06-25T15:24:33,809 Building wheels for collected packages: ont-spectre 2024-06-25T15:24:33,813 Created temporary directory: /tmp/pip-wheel-abn68d8r 2024-06-25T15:24:33,814 Building wheel for ont-spectre (setup.py): started 2024-06-25T15:24:33,815 Destination directory: /tmp/pip-wheel-abn68d8r 2024-06-25T15:24:33,816 Running command python setup.py bdist_wheel 2024-06-25T15:24:34,328 /tmp/pip-wheel-j23t1tay/ont-spectre_e075047e9a3a4ff09bc372c6c3781382/setup.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-06-25T15:24:34,328 import pkg_resources 2024-06-25T15:24:34,929 running bdist_wheel 2024-06-25T15:24:35,069 running build 2024-06-25T15:24:35,069 running build_py 2024-06-25T15:24:35,101 creating build 2024-06-25T15:24:35,102 creating build/lib 2024-06-25T15:24:35,102 creating build/lib/spectre 2024-06-25T15:24:35,104 copying spectre/__init__.py -> build/lib/spectre 2024-06-25T15:24:35,106 copying spectre/spectreCNVPopulation.py -> build/lib/spectre 2024-06-25T15:24:35,108 copying spectre/spectreCNV.py -> build/lib/spectre 2024-06-25T15:24:35,110 copying spectre/main.py -> build/lib/spectre 2024-06-25T15:24:35,114 creating build/lib/spectre/plots 2024-06-25T15:24:35,115 copying spectre/plots/plot.py -> build/lib/spectre/plots 2024-06-25T15:24:35,117 copying spectre/plots/__init__.py -> build/lib/spectre/plots 2024-06-25T15:24:35,119 creating build/lib/spectre/util 2024-06-25T15:24:35,120 copying spectre/util/cnv_id.py -> build/lib/spectre/util 2024-06-25T15:24:35,122 copying spectre/util/dataAnalyzer.py -> build/lib/spectre/util 2024-06-25T15:24:35,124 copying spectre/util/mosdepthReader.py -> build/lib/spectre/util 2024-06-25T15:24:35,126 copying spectre/util/OSUtil.py -> build/lib/spectre/util 2024-06-25T15:24:35,128 copying spectre/util/vcf_parser.py -> build/lib/spectre/util 2024-06-25T15:24:35,130 copying spectre/util/__init__.py -> build/lib/spectre/util 2024-06-25T15:24:35,132 copying spectre/util/outputWriter.py -> build/lib/spectre/util 2024-06-25T15:24:35,134 creating build/lib/spectre/analysis 2024-06-25T15:24:35,135 copying spectre/analysis/call_cnv_coverage.py -> build/lib/spectre/analysis 2024-06-25T15:24:35,138 copying spectre/analysis/cnv_candidate.py -> build/lib/spectre/analysis 2024-06-25T15:24:35,140 copying spectre/analysis/coverage_stats.py -> build/lib/spectre/analysis 2024-06-25T15:24:35,142 copying spectre/analysis/__init__.py -> build/lib/spectre/analysis 2024-06-25T15:24:35,143 copying spectre/analysis/call_cnv_AF.py -> build/lib/spectre/analysis 2024-06-25T15:24:35,145 copying spectre/analysis/cnv_metrics.py -> build/lib/spectre/analysis 2024-06-25T15:24:35,148 copying spectre/analysis/analysis.py -> build/lib/spectre/analysis 2024-06-25T15:24:35,151 creating build/lib/spectre/util/metadata 2024-06-25T15:24:35,152 copying spectre/util/metadata/metadataCollector.py -> build/lib/spectre/util/metadata 2024-06-25T15:24:35,154 copying spectre/util/metadata/__init__.py -> build/lib/spectre/util/metadata 2024-06-25T15:24:35,158 creating build/lib/spectre/data 2024-06-25T15:24:35,159 copying spectre/data/grch38_blacklist_0.3.bed -> build/lib/spectre/data 2024-06-25T15:24:35,164 copying spectre/data/grch38_metadata.mdr -> build/lib/spectre/data 2024-06-25T15:24:35,197 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-06-25T15:24:35,198 !! 2024-06-25T15:24:35,199 ******************************************************************************** 2024-06-25T15:24:35,199 Please avoid running ``setup.py`` directly. 2024-06-25T15:24:35,200 Instead, use pypa/build, pypa/installer or other 2024-06-25T15:24:35,200 standards-based tools. 2024-06-25T15:24:35,201 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-06-25T15:24:35,202 ******************************************************************************** 2024-06-25T15:24:35,203 !! 2024-06-25T15:24:35,203 self.initialize_options() 2024-06-25T15:24:35,226 installing to build/bdist.linux-armv7l/wheel 2024-06-25T15:24:35,226 running install 2024-06-25T15:24:35,251 running install_lib 2024-06-25T15:24:35,279 creating build/bdist.linux-armv7l 2024-06-25T15:24:35,279 creating build/bdist.linux-armv7l/wheel 2024-06-25T15:24:35,281 creating build/bdist.linux-armv7l/wheel/spectre 2024-06-25T15:24:35,282 creating build/bdist.linux-armv7l/wheel/spectre/plots 2024-06-25T15:24:35,284 copying build/lib/spectre/plots/plot.py -> build/bdist.linux-armv7l/wheel/spectre/plots 2024-06-25T15:24:35,286 copying build/lib/spectre/plots/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/plots 2024-06-25T15:24:35,288 creating build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,289 copying build/lib/spectre/util/cnv_id.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,291 copying build/lib/spectre/util/dataAnalyzer.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,294 creating build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-06-25T15:24:35,295 copying build/lib/spectre/util/metadata/metadataCollector.py -> build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-06-25T15:24:35,297 copying build/lib/spectre/util/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-06-25T15:24:35,299 copying build/lib/spectre/util/mosdepthReader.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,301 copying build/lib/spectre/util/OSUtil.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,303 copying build/lib/spectre/util/vcf_parser.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,305 copying build/lib/spectre/util/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,307 copying build/lib/spectre/util/outputWriter.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-25T15:24:35,310 creating build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,311 copying build/lib/spectre/analysis/call_cnv_coverage.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,313 copying build/lib/spectre/analysis/cnv_candidate.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,315 copying build/lib/spectre/analysis/coverage_stats.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,317 copying build/lib/spectre/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,318 copying build/lib/spectre/analysis/call_cnv_AF.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,320 copying build/lib/spectre/analysis/cnv_metrics.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,323 copying build/lib/spectre/analysis/analysis.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-25T15:24:35,326 copying build/lib/spectre/__init__.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-25T15:24:35,328 creating build/bdist.linux-armv7l/wheel/spectre/data 2024-06-25T15:24:35,329 copying build/lib/spectre/data/grch38_blacklist_0.3.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-06-25T15:24:35,335 copying build/lib/spectre/data/grch38_metadata.mdr -> build/bdist.linux-armv7l/wheel/spectre/data 2024-06-25T15:24:35,338 copying build/lib/spectre/spectreCNVPopulation.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-25T15:24:35,340 copying build/lib/spectre/spectreCNV.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-25T15:24:35,343 copying build/lib/spectre/main.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-25T15:24:35,345 running install_egg_info 2024-06-25T15:24:35,378 running egg_info 2024-06-25T15:24:35,405 writing ont_spectre.egg-info/PKG-INFO 2024-06-25T15:24:35,408 writing dependency_links to ont_spectre.egg-info/dependency_links.txt 2024-06-25T15:24:35,410 writing entry points to ont_spectre.egg-info/entry_points.txt 2024-06-25T15:24:35,411 writing requirements to ont_spectre.egg-info/requires.txt 2024-06-25T15:24:35,413 writing top-level names to ont_spectre.egg-info/top_level.txt 2024-06-25T15:24:35,446 reading manifest file 'ont_spectre.egg-info/SOURCES.txt' 2024-06-25T15:24:35,449 reading manifest template 'MANIFEST.in' 2024-06-25T15:24:35,450 adding license file 'LICENSE.md' 2024-06-25T15:24:35,453 writing manifest file 'ont_spectre.egg-info/SOURCES.txt' 2024-06-25T15:24:35,455 Copying ont_spectre.egg-info to build/bdist.linux-armv7l/wheel/ont_spectre-0.2.2-py3.11.egg-info 2024-06-25T15:24:35,470 running install_scripts 2024-06-25T15:24:35,487 creating build/bdist.linux-armv7l/wheel/ont_spectre-0.2.2.dist-info/WHEEL 2024-06-25T15:24:35,490 creating '/tmp/pip-wheel-abn68d8r/ont_spectre-0.2.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-25T15:24:35,494 adding 'spectre/__init__.py' 2024-06-25T15:24:35,497 adding 'spectre/main.py' 2024-06-25T15:24:35,499 adding 'spectre/spectreCNV.py' 2024-06-25T15:24:35,502 adding 'spectre/spectreCNVPopulation.py' 2024-06-25T15:24:35,504 adding 'spectre/analysis/__init__.py' 2024-06-25T15:24:35,508 adding 'spectre/analysis/analysis.py' 2024-06-25T15:24:35,510 adding 'spectre/analysis/call_cnv_AF.py' 2024-06-25T15:24:35,512 adding 'spectre/analysis/call_cnv_coverage.py' 2024-06-25T15:24:35,514 adding 'spectre/analysis/cnv_candidate.py' 2024-06-25T15:24:35,517 adding 'spectre/analysis/cnv_metrics.py' 2024-06-25T15:24:35,518 adding 'spectre/analysis/coverage_stats.py' 2024-06-25T15:24:35,542 adding 'spectre/data/grch38_blacklist_0.3.bed' 2024-06-25T15:24:35,549 adding 'spectre/data/grch38_metadata.mdr' 2024-06-25T15:24:35,551 adding 'spectre/plots/__init__.py' 2024-06-25T15:24:35,552 adding 'spectre/plots/plot.py' 2024-06-25T15:24:35,555 adding 'spectre/util/OSUtil.py' 2024-06-25T15:24:35,556 adding 'spectre/util/__init__.py' 2024-06-25T15:24:35,557 adding 'spectre/util/cnv_id.py' 2024-06-25T15:24:35,559 adding 'spectre/util/dataAnalyzer.py' 2024-06-25T15:24:35,561 adding 'spectre/util/mosdepthReader.py' 2024-06-25T15:24:35,563 adding 'spectre/util/outputWriter.py' 2024-06-25T15:24:35,565 adding 'spectre/util/vcf_parser.py' 2024-06-25T15:24:35,567 adding 'spectre/util/metadata/__init__.py' 2024-06-25T15:24:35,569 adding 'spectre/util/metadata/metadataCollector.py' 2024-06-25T15:24:35,572 adding 'ont_spectre-0.2.2.dist-info/LICENSE.md' 2024-06-25T15:24:35,573 adding 'ont_spectre-0.2.2.dist-info/METADATA' 2024-06-25T15:24:35,574 adding 'ont_spectre-0.2.2.dist-info/WHEEL' 2024-06-25T15:24:35,576 adding 'ont_spectre-0.2.2.dist-info/entry_points.txt' 2024-06-25T15:24:35,577 adding 'ont_spectre-0.2.2.dist-info/top_level.txt' 2024-06-25T15:24:35,578 adding 'ont_spectre-0.2.2.dist-info/RECORD' 2024-06-25T15:24:35,581 removing build/bdist.linux-armv7l/wheel 2024-06-25T15:24:35,715 Building wheel for ont-spectre (setup.py): finished with status 'done' 2024-06-25T15:24:35,719 Created wheel for ont-spectre: filename=ont_spectre-0.2.2-py3-none-any.whl size=95089 sha256=5232bb16552b99c81c7f9c253aec88f7cbe0ac3d4ec343f78edbf73121cf9c2a 2024-06-25T15:24:35,720 Stored in directory: /tmp/pip-ephem-wheel-cache-ghjpph4w/wheels/0f/9d/a1/4824feeb80019bffe206d3b7eb92c1983952b08110f2508114 2024-06-25T15:24:35,731 Successfully built ont-spectre 2024-06-25T15:24:35,736 Removed build tracker: '/tmp/pip-build-tracker-2r7pq12y'