2024-06-03T13:24:11,303 Created temporary directory: /tmp/pip-build-tracker-boxmnzqi 2024-06-03T13:24:11,304 Initialized build tracking at /tmp/pip-build-tracker-boxmnzqi 2024-06-03T13:24:11,305 Created build tracker: /tmp/pip-build-tracker-boxmnzqi 2024-06-03T13:24:11,305 Entered build tracker: /tmp/pip-build-tracker-boxmnzqi 2024-06-03T13:24:11,306 Created temporary directory: /tmp/pip-wheel-im0vjgii 2024-06-03T13:24:11,309 Created temporary directory: /tmp/pip-ephem-wheel-cache-zw9h2wdm 2024-06-03T13:24:11,334 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-03T13:24:11,337 2 location(s) to search for versions of ont-spectre: 2024-06-03T13:24:11,337 * https://pypi.org/simple/ont-spectre/ 2024-06-03T13:24:11,337 * https://www.piwheels.org/simple/ont-spectre/ 2024-06-03T13:24:11,338 Fetching project page and analyzing links: https://pypi.org/simple/ont-spectre/ 2024-06-03T13:24:11,339 Getting page https://pypi.org/simple/ont-spectre/ 2024-06-03T13:24:11,340 Found index url https://pypi.org/simple/ 2024-06-03T13:24:11,564 Fetched page https://pypi.org/simple/ont-spectre/ as application/vnd.pypi.simple.v1+json 2024-06-03T13:24:11,565 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 2024-06-03T13:24:11,566 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 2024-06-03T13:24:11,567 Fetching project page and analyzing links: https://www.piwheels.org/simple/ont-spectre/ 2024-06-03T13:24:11,567 Getting page https://www.piwheels.org/simple/ont-spectre/ 2024-06-03T13:24:11,569 Found index url https://www.piwheels.org/simple/ 2024-06-03T13:24:11,723 Fetched page https://www.piwheels.org/simple/ont-spectre/ as text/html 2024-06-03T13:24:11,725 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/) 2024-06-03T13:24:11,726 Skipping link: not a file: https://www.piwheels.org/simple/ont-spectre/ 2024-06-03T13:24:11,727 Skipping link: not a file: https://pypi.org/simple/ont-spectre/ 2024-06-03T13:24:11,745 Given no hashes to check 1 links for project 'ont-spectre': discarding no candidates 2024-06-03T13:24:11,763 Collecting ont-spectre==0.2.1 2024-06-03T13:24:11,766 Created temporary directory: /tmp/pip-unpack-3_hb_m7b 2024-06-03T13:24:11,989 Downloading ont_spectre-0.2.1.tar.gz (89 kB) 2024-06-03T13:24:12,139 Added ont-spectre==0.2.1 from https://files.pythonhosted.org/packages/c1/f1/1629482a61c0ee61f830cbcd418e0660c4fd2bbf3c4ba5584e3476ee0bf6/ont_spectre-0.2.1.tar.gz to build tracker '/tmp/pip-build-tracker-boxmnzqi' 2024-06-03T13:24:12,142 Running setup.py (path:/tmp/pip-wheel-im0vjgii/ont-spectre_25c5a37fa994403ba01a98693e0025ee/setup.py) egg_info for package ont-spectre 2024-06-03T13:24:12,143 Created temporary directory: /tmp/pip-pip-egg-info-ul0fqjaj 2024-06-03T13:24:12,143 Preparing metadata (setup.py): started 2024-06-03T13:24:12,144 Running command python setup.py egg_info 2024-06-03T13:24:12,696 /tmp/pip-wheel-im0vjgii/ont-spectre_25c5a37fa994403ba01a98693e0025ee/setup.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-06-03T13:24:12,696 import pkg_resources 2024-06-03T13:24:13,278 running egg_info 2024-06-03T13:24:13,280 creating /tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info 2024-06-03T13:24:13,304 writing /tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/PKG-INFO 2024-06-03T13:24:13,307 writing dependency_links to /tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/dependency_links.txt 2024-06-03T13:24:13,309 writing entry points to /tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/entry_points.txt 2024-06-03T13:24:13,312 writing requirements to /tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/requires.txt 2024-06-03T13:24:13,313 writing top-level names to /tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/top_level.txt 2024-06-03T13:24:13,314 writing manifest file '/tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/SOURCES.txt' 2024-06-03T13:24:13,399 reading manifest file '/tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/SOURCES.txt' 2024-06-03T13:24:13,400 reading manifest template 'MANIFEST.in' 2024-06-03T13:24:13,401 adding license file 'LICENSE.md' 2024-06-03T13:24:13,404 writing manifest file '/tmp/pip-pip-egg-info-ul0fqjaj/ont_spectre.egg-info/SOURCES.txt' 2024-06-03T13:24:13,521 Preparing metadata (setup.py): finished with status 'done' 2024-06-03T13:24:13,525 Source in /tmp/pip-wheel-im0vjgii/ont-spectre_25c5a37fa994403ba01a98693e0025ee has version 0.2.1, which satisfies requirement ont-spectre==0.2.1 from https://files.pythonhosted.org/packages/c1/f1/1629482a61c0ee61f830cbcd418e0660c4fd2bbf3c4ba5584e3476ee0bf6/ont_spectre-0.2.1.tar.gz 2024-06-03T13:24:13,526 Removed ont-spectre==0.2.1 from https://files.pythonhosted.org/packages/c1/f1/1629482a61c0ee61f830cbcd418e0660c4fd2bbf3c4ba5584e3476ee0bf6/ont_spectre-0.2.1.tar.gz from build tracker '/tmp/pip-build-tracker-boxmnzqi' 2024-06-03T13:24:13,530 Created temporary directory: /tmp/pip-unpack-bcwup5zw 2024-06-03T13:24:13,531 Created temporary directory: /tmp/pip-unpack-w14y_8ra 2024-06-03T13:24:13,542 Building wheels for collected packages: ont-spectre 2024-06-03T13:24:13,546 Created temporary directory: /tmp/pip-wheel-7sut8mzy 2024-06-03T13:24:13,546 Building wheel for ont-spectre (setup.py): started 2024-06-03T13:24:13,547 Destination directory: /tmp/pip-wheel-7sut8mzy 2024-06-03T13:24:13,548 Running command python setup.py bdist_wheel 2024-06-03T13:24:14,047 /tmp/pip-wheel-im0vjgii/ont-spectre_25c5a37fa994403ba01a98693e0025ee/setup.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-06-03T13:24:14,047 import pkg_resources 2024-06-03T13:24:14,604 running bdist_wheel 2024-06-03T13:24:14,697 running build 2024-06-03T13:24:14,698 running build_py 2024-06-03T13:24:14,724 creating build 2024-06-03T13:24:14,725 creating build/lib 2024-06-03T13:24:14,725 creating build/lib/spectre 2024-06-03T13:24:14,726 copying spectre/__init__.py -> build/lib/spectre 2024-06-03T13:24:14,728 copying spectre/spectreCNVPopulation.py -> build/lib/spectre 2024-06-03T13:24:14,731 copying spectre/spectreCNV.py -> build/lib/spectre 2024-06-03T13:24:14,733 copying spectre/main.py -> build/lib/spectre 2024-06-03T13:24:14,736 creating build/lib/spectre/util 2024-06-03T13:24:14,737 copying spectre/util/outputWriter.py -> build/lib/spectre/util 2024-06-03T13:24:14,739 copying spectre/util/mosdepthReader.py -> build/lib/spectre/util 2024-06-03T13:24:14,741 copying spectre/util/__init__.py -> build/lib/spectre/util 2024-06-03T13:24:14,742 copying spectre/util/OSUtil.py -> build/lib/spectre/util 2024-06-03T13:24:14,744 copying spectre/util/dataAnalyzer.py -> build/lib/spectre/util 2024-06-03T13:24:14,745 copying spectre/util/cnv_id.py -> build/lib/spectre/util 2024-06-03T13:24:14,747 copying spectre/util/vcf_parser.py -> build/lib/spectre/util 2024-06-03T13:24:14,750 creating build/lib/spectre/plots 2024-06-03T13:24:14,751 copying spectre/plots/__init__.py -> build/lib/spectre/plots 2024-06-03T13:24:14,752 copying spectre/plots/plot.py -> build/lib/spectre/plots 2024-06-03T13:24:14,755 creating build/lib/spectre/analysis 2024-06-03T13:24:14,756 copying spectre/analysis/cnv_metrics.py -> build/lib/spectre/analysis 2024-06-03T13:24:14,758 copying spectre/analysis/__init__.py -> build/lib/spectre/analysis 2024-06-03T13:24:14,760 copying spectre/analysis/call_cnv_AF.py -> build/lib/spectre/analysis 2024-06-03T13:24:14,762 copying spectre/analysis/coverage_stats.py -> build/lib/spectre/analysis 2024-06-03T13:24:14,764 copying spectre/analysis/analysis.py -> build/lib/spectre/analysis 2024-06-03T13:24:14,767 copying spectre/analysis/cnv_candidate.py -> build/lib/spectre/analysis 2024-06-03T13:24:14,768 copying spectre/analysis/call_cnv_coverage.py -> build/lib/spectre/analysis 2024-06-03T13:24:14,771 creating build/lib/spectre/util/metadata 2024-06-03T13:24:14,771 copying spectre/util/metadata/metadataCollector.py -> build/lib/spectre/util/metadata 2024-06-03T13:24:14,773 copying spectre/util/metadata/__init__.py -> build/lib/spectre/util/metadata 2024-06-03T13:24:14,777 creating build/lib/spectre/data 2024-06-03T13:24:14,778 copying spectre/data/grch38_blacklist_0.3.bed -> build/lib/spectre/data 2024-06-03T13:24:14,788 copying spectre/data/grch38_metadata.mdr -> build/lib/spectre/data 2024-06-03T13:24:14,818 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-06-03T13:24:14,819 !! 2024-06-03T13:24:14,820 ******************************************************************************** 2024-06-03T13:24:14,820 Please avoid running ``setup.py`` directly. 2024-06-03T13:24:14,821 Instead, use pypa/build, pypa/installer or other 2024-06-03T13:24:14,821 standards-based tools. 2024-06-03T13:24:14,822 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-06-03T13:24:14,823 ******************************************************************************** 2024-06-03T13:24:14,824 !! 2024-06-03T13:24:14,825 self.initialize_options() 2024-06-03T13:24:14,846 installing to build/bdist.linux-armv7l/wheel 2024-06-03T13:24:14,846 running install 2024-06-03T13:24:14,871 running install_lib 2024-06-03T13:24:14,895 creating build/bdist.linux-armv7l 2024-06-03T13:24:14,896 creating build/bdist.linux-armv7l/wheel 2024-06-03T13:24:14,897 creating build/bdist.linux-armv7l/wheel/spectre 2024-06-03T13:24:14,898 creating build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,899 copying build/lib/spectre/util/outputWriter.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,902 copying build/lib/spectre/util/mosdepthReader.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,904 copying build/lib/spectre/util/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,905 copying build/lib/spectre/util/OSUtil.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,907 copying build/lib/spectre/util/dataAnalyzer.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,909 creating build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-06-03T13:24:14,910 copying build/lib/spectre/util/metadata/metadataCollector.py -> build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-06-03T13:24:14,912 copying build/lib/spectre/util/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-06-03T13:24:14,914 copying build/lib/spectre/util/cnv_id.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,916 copying build/lib/spectre/util/vcf_parser.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-06-03T13:24:14,918 creating build/bdist.linux-armv7l/wheel/spectre/plots 2024-06-03T13:24:14,919 copying build/lib/spectre/plots/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/plots 2024-06-03T13:24:14,921 copying build/lib/spectre/plots/plot.py -> build/bdist.linux-armv7l/wheel/spectre/plots 2024-06-03T13:24:14,923 copying build/lib/spectre/__init__.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-03T13:24:14,925 creating build/bdist.linux-armv7l/wheel/spectre/data 2024-06-03T13:24:14,926 copying build/lib/spectre/data/grch38_blacklist_0.3.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-06-03T13:24:14,931 copying build/lib/spectre/data/grch38_metadata.mdr -> build/bdist.linux-armv7l/wheel/spectre/data 2024-06-03T13:24:14,933 copying build/lib/spectre/spectreCNVPopulation.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-03T13:24:14,936 creating build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,937 copying build/lib/spectre/analysis/cnv_metrics.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,940 copying build/lib/spectre/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,941 copying build/lib/spectre/analysis/call_cnv_AF.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,943 copying build/lib/spectre/analysis/coverage_stats.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,945 copying build/lib/spectre/analysis/analysis.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,948 copying build/lib/spectre/analysis/cnv_candidate.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,949 copying build/lib/spectre/analysis/call_cnv_coverage.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-06-03T13:24:14,952 copying build/lib/spectre/spectreCNV.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-03T13:24:14,954 copying build/lib/spectre/main.py -> build/bdist.linux-armv7l/wheel/spectre 2024-06-03T13:24:14,956 running install_egg_info 2024-06-03T13:24:15,020 running egg_info 2024-06-03T13:24:15,045 writing ont_spectre.egg-info/PKG-INFO 2024-06-03T13:24:15,047 writing dependency_links to ont_spectre.egg-info/dependency_links.txt 2024-06-03T13:24:15,049 writing entry points to ont_spectre.egg-info/entry_points.txt 2024-06-03T13:24:15,050 writing requirements to ont_spectre.egg-info/requires.txt 2024-06-03T13:24:15,051 writing top-level names to ont_spectre.egg-info/top_level.txt 2024-06-03T13:24:15,082 reading manifest file 'ont_spectre.egg-info/SOURCES.txt' 2024-06-03T13:24:15,084 reading manifest template 'MANIFEST.in' 2024-06-03T13:24:15,085 adding license file 'LICENSE.md' 2024-06-03T13:24:15,088 writing manifest file 'ont_spectre.egg-info/SOURCES.txt' 2024-06-03T13:24:15,089 Copying ont_spectre.egg-info to build/bdist.linux-armv7l/wheel/ont_spectre-0.2.1-py3.11.egg-info 2024-06-03T13:24:15,101 running install_scripts 2024-06-03T13:24:15,117 creating build/bdist.linux-armv7l/wheel/ont_spectre-0.2.1.dist-info/WHEEL 2024-06-03T13:24:15,119 creating '/tmp/pip-wheel-7sut8mzy/ont_spectre-0.2.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-03T13:24:15,122 adding 'spectre/__init__.py' 2024-06-03T13:24:15,126 adding 'spectre/main.py' 2024-06-03T13:24:15,128 adding 'spectre/spectreCNV.py' 2024-06-03T13:24:15,129 adding 'spectre/spectreCNVPopulation.py' 2024-06-03T13:24:15,131 adding 'spectre/analysis/__init__.py' 2024-06-03T13:24:15,135 adding 'spectre/analysis/analysis.py' 2024-06-03T13:24:15,137 adding 'spectre/analysis/call_cnv_AF.py' 2024-06-03T13:24:15,139 adding 'spectre/analysis/call_cnv_coverage.py' 2024-06-03T13:24:15,140 adding 'spectre/analysis/cnv_candidate.py' 2024-06-03T13:24:15,143 adding 'spectre/analysis/cnv_metrics.py' 2024-06-03T13:24:15,144 adding 'spectre/analysis/coverage_stats.py' 2024-06-03T13:24:15,167 adding 'spectre/data/grch38_blacklist_0.3.bed' 2024-06-03T13:24:15,173 adding 'spectre/data/grch38_metadata.mdr' 2024-06-03T13:24:15,174 adding 'spectre/plots/__init__.py' 2024-06-03T13:24:15,176 adding 'spectre/plots/plot.py' 2024-06-03T13:24:15,178 adding 'spectre/util/OSUtil.py' 2024-06-03T13:24:15,179 adding 'spectre/util/__init__.py' 2024-06-03T13:24:15,180 adding 'spectre/util/cnv_id.py' 2024-06-03T13:24:15,181 adding 'spectre/util/dataAnalyzer.py' 2024-06-03T13:24:15,182 adding 'spectre/util/mosdepthReader.py' 2024-06-03T13:24:15,184 adding 'spectre/util/outputWriter.py' 2024-06-03T13:24:15,186 adding 'spectre/util/vcf_parser.py' 2024-06-03T13:24:15,188 adding 'spectre/util/metadata/__init__.py' 2024-06-03T13:24:15,189 adding 'spectre/util/metadata/metadataCollector.py' 2024-06-03T13:24:15,192 adding 'ont_spectre-0.2.1.dist-info/LICENSE.md' 2024-06-03T13:24:15,193 adding 'ont_spectre-0.2.1.dist-info/METADATA' 2024-06-03T13:24:15,194 adding 'ont_spectre-0.2.1.dist-info/WHEEL' 2024-06-03T13:24:15,195 adding 'ont_spectre-0.2.1.dist-info/entry_points.txt' 2024-06-03T13:24:15,196 adding 'ont_spectre-0.2.1.dist-info/top_level.txt' 2024-06-03T13:24:15,197 adding 'ont_spectre-0.2.1.dist-info/RECORD' 2024-06-03T13:24:15,199 removing build/bdist.linux-armv7l/wheel 2024-06-03T13:24:15,329 Building wheel for ont-spectre (setup.py): finished with status 'done' 2024-06-03T13:24:15,332 Created wheel for ont-spectre: filename=ont_spectre-0.2.1-py3-none-any.whl size=95109 sha256=a7f8610fcbbed8148b3c869c141ba7400ba551fb08b1634b12a9d0e611c2e252 2024-06-03T13:24:15,334 Stored in directory: /tmp/pip-ephem-wheel-cache-zw9h2wdm/wheels/4e/78/38/ccd0be8b48dd8a11b9ac7e54bb008d8d24445addce3c93dfc0 2024-06-03T13:24:15,344 Successfully built ont-spectre 2024-06-03T13:24:15,350 Removed build tracker: '/tmp/pip-build-tracker-boxmnzqi'