=>> Building biology/py-gffutils
build started at Sun May  4 17:16:30 EDT 2025
port directory: /usr/ports/biology/py-gffutils
package name: py311-gffutils-0.13_1
building for: FreeBSD 13amd64-weekly-desktop-job-02 13.4-RELEASE-p4 FreeBSD 13.4-RELEASE-p4 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root  wheel  937 Mar 20 01:40 /usr/ports/biology/py-gffutils/Makefile
Ports top last git commit: 57a50b106b87
Ports top unclean checkout: yes
Port dir last git commit: 06a08e69f3ac
Port dir unclean checkout: no
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Host OSVERSION: 1402000
Jail OSVERSION: 1304000
Job Id: 02

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--MAINTAINER--
yuri@FreeBSD.org
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--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
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=======================<phase: check-sanity   >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===========================================================================
=======================<phase: pkg-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py311-gffutils-0.13_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-2.0.6.pkg
[13amd64-weekly-desktop-job-02] Installing pkg-2.0.6...
[13amd64-weekly-desktop-job-02] Extracting pkg-2.0.6: .......... done
===>   py311-gffutils-0.13_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py311-gffutils-0.13_1
===========================================================================
=======================<phase: fetch-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch          >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Fetching all distfiles required by py311-gffutils-0.13_1 for building
===========================================================================
=======================<phase: checksum       >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Fetching all distfiles required by py311-gffutils-0.13_1 for building
=> SHA256 Checksum OK for gffutils-0.13.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract        >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===> Fetching all distfiles required by py311-gffutils-0.13_1 for building
===>  Extracting for py311-gffutils-0.13_1
=> SHA256 Checksum OK for gffutils-0.13.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch          >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  Patching for py311-gffutils-0.13_1
===========================================================================
=======================<phase: build-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py311-gffutils-0.13_1 depends on package: py311-setuptools>=63.1.0 - not found
===>   Installing existing package /packages/All/py311-setuptools-63.1.0_2.pkg
[13amd64-weekly-desktop-job-02] Installing py311-setuptools-63.1.0_2...
[13amd64-weekly-desktop-job-02] `-- Installing python311-3.11.11...
[13amd64-weekly-desktop-job-02] |   `-- Installing gettext-runtime-0.23.1...
[13amd64-weekly-desktop-job-02] |   | `-- Installing indexinfo-0.3.1_1...
[13amd64-weekly-desktop-job-02] |   | `-- Extracting indexinfo-0.3.1_1: . done
[13amd64-weekly-desktop-job-02] |   `-- Extracting gettext-runtime-0.23.1: .......... done
[13amd64-weekly-desktop-job-02] |   `-- Installing libffi-3.4.6...
[13amd64-weekly-desktop-job-02] |   `-- Extracting libffi-3.4.6: .......... done
[13amd64-weekly-desktop-job-02] |   `-- Installing mpdecimal-4.0.0...
[13amd64-weekly-desktop-job-02] |   `-- Extracting mpdecimal-4.0.0: .......... done
[13amd64-weekly-desktop-job-02] |   `-- Installing readline-8.2.13_2...
[13amd64-weekly-desktop-job-02] |   `-- Extracting readline-8.2.13_2: .......... done
[13amd64-weekly-desktop-job-02] `-- Extracting python311-3.11.11: .......... done
[13amd64-weekly-desktop-job-02] Extracting py311-setuptools-63.1.0_2: .......... done
=====
Message from python311-3.11.11:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py311-gdbm       databases/py-gdbm@py311
py311-sqlite3    databases/py-sqlite3@py311
py311-tkinter    x11-toolkits/py-tkinter@py311
===>   py311-gffutils-0.13_1 depends on package: py311-setuptools>=63.1.0 - found
===>   Returning to build of py311-gffutils-0.13_1
===>   py311-gffutils-0.13_1 depends on file: /usr/local/bin/python3.11 - found
===========================================================================
=======================<phase: lib-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure      >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  Configuring for py311-gffutils-0.13_1
/usr/local/lib/python3.11/site-packages/setuptools/dist.py:530: UserWarning: Normalizing ' 0.13' to '0.13'
  warnings.warn(tmpl.format(**locals()))
running config
===========================================================================
=======================<phase: build          >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  Building for py311-gffutils-0.13_1
/usr/local/lib/python3.11/site-packages/setuptools/dist.py:530: UserWarning: Normalizing ' 0.13' to '0.13'
  warnings.warn(tmpl.format(**locals()))
running build
running build_py
creating build
creating build/lib
creating build/lib/gffutils
copying gffutils/attributes.py -> build/lib/gffutils
copying gffutils/helpers.py -> build/lib/gffutils
copying gffutils/gffwriter.py -> build/lib/gffutils
copying gffutils/pybedtools_integration.py -> build/lib/gffutils
copying gffutils/iterators.py -> build/lib/gffutils
copying gffutils/__init__.py -> build/lib/gffutils
copying gffutils/interface.py -> build/lib/gffutils
copying gffutils/version.py -> build/lib/gffutils
copying gffutils/inspect.py -> build/lib/gffutils
copying gffutils/feature.py -> build/lib/gffutils
copying gffutils/merge_criteria.py -> build/lib/gffutils
copying gffutils/bins.py -> build/lib/gffutils
copying gffutils/constants.py -> build/lib/gffutils
copying gffutils/biopython_integration.py -> build/lib/gffutils
copying gffutils/parser.py -> build/lib/gffutils
copying gffutils/exceptions.py -> build/lib/gffutils
copying gffutils/convert.py -> build/lib/gffutils
copying gffutils/create.py -> build/lib/gffutils
creating build/lib/gffutils/scripts
copying gffutils/scripts/gffutils-flybase-convert.py -> build/lib/gffutils/scripts
creating build/lib/gffutils/test
copying gffutils/test/test_merge.py -> build/lib/gffutils/test
copying gffutils/test/test_1.py -> build/lib/gffutils/test
copying gffutils/test/conftest.py -> build/lib/gffutils/test
copying gffutils/test/helpers_test.py -> build/lib/gffutils/test
copying gffutils/test/__init__.py -> build/lib/gffutils/test
copying gffutils/test/feature_test.py -> build/lib/gffutils/test
copying gffutils/test/test_cli.py -> build/lib/gffutils/test
copying gffutils/test/test_issues.py -> build/lib/gffutils/test
copying gffutils/test/test_biopython_integration.py -> build/lib/gffutils/test
copying gffutils/test/synth_test_base.py -> build/lib/gffutils/test
copying gffutils/test/parser_test.py -> build/lib/gffutils/test
copying gffutils/test/test_merge_all.py -> build/lib/gffutils/test
copying gffutils/test/attr_test_cases.py -> build/lib/gffutils/test
copying gffutils/test/test_iterators.py -> build/lib/gffutils/test
copying gffutils/test/performance_evaluation.py -> build/lib/gffutils/test
copying gffutils/test/expected.py -> build/lib/gffutils/test
creating build/lib/gffutils/test/data
copying gffutils/test/data/keep-order-test.gtf -> build/lib/gffutils/test/data
copying gffutils/test/data/gff_example1.gff3 -> build/lib/gffutils/test/data
copying gffutils/test/data/gff_example1.gff3.gz -> build/lib/gffutils/test/data
copying gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/synthetic.gff3 -> build/lib/gffutils/test/data
copying gffutils/test/data/gencode-v19.gtf -> build/lib/gffutils/test/data
copying gffutils/test/data/dm6-chr2L.fa.fai -> build/lib/gffutils/test/data
copying gffutils/test/data/sharr.gtf -> build/lib/gffutils/test/data
copying gffutils/test/data/F3-unique-3.v2.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/jgi_gff2.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/gms2_example.gff3 -> build/lib/gffutils/test/data
copying gffutils/test/data/dm6-chr2L.fa -> build/lib/gffutils/test/data
copying gffutils/test/data/issue167.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/wormbase_gff2_alt.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/keyval_sep_in_attrs.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/issue_197.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/intro_docs_example.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/mouse_extra_comma.gff3 -> build/lib/gffutils/test/data
copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/FBgn0031208.gtf.db -> build/lib/gffutils/test/data
copying gffutils/test/data/nonascii -> build/lib/gffutils/test/data
copying gffutils/test/data/FBgn0031208.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/download-large-annotation-files.sh -> build/lib/gffutils/test/data
copying gffutils/test/data/ncbi_gff3.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/gencode.vM8.chromsizes.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/ensembl_gtf.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/hybrid1.gff3 -> build/lib/gffutils/test/data
copying gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> build/lib/gffutils/test/data
copying gffutils/test/data/FBgn0031208.gtf -> build/lib/gffutils/test/data
copying gffutils/test/data/wormbase_gff2.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/random-chr.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/glimmer_nokeyval.gff3 -> build/lib/gffutils/test/data
copying gffutils/test/data/issue174.gtf -> build/lib/gffutils/test/data
copying gffutils/test/data/unsanitized.gff -> build/lib/gffutils/test/data
copying gffutils/test/data/c_elegans_WS199_ann_gff.txt -> build/lib/gffutils/test/data
copying gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> build/lib/gffutils/test/data
running build_scripts
creating build/scripts-3.11
copying and adjusting gffutils/scripts/gffutils-cli -> build/scripts-3.11
changing mode of build/scripts-3.11/gffutils-cli from 644 to 755
===========================================================================
=======================<phase: run-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py311-gffutils-0.13_1 depends on package: py311-argcomplete>=1.9.4 - not found
===>   Installing existing package /packages/All/py311-argcomplete-3.6.0.pkg
[13amd64-weekly-desktop-job-02] Installing py311-argcomplete-3.6.0...
[13amd64-weekly-desktop-job-02] Extracting py311-argcomplete-3.6.0: .......... done
===>   py311-gffutils-0.13_1 depends on package: py311-argcomplete>=1.9.4 - found
===>   Returning to build of py311-gffutils-0.13_1
===>   py311-gffutils-0.13_1 depends on package: py311-argh>=0.26.2 - not found
===>   Installing existing package /packages/All/py311-argh-0.31.3.pkg
[13amd64-weekly-desktop-job-02] Installing py311-argh-0.31.3...
[13amd64-weekly-desktop-job-02] Extracting py311-argh-0.31.3: .......... done
===>   py311-gffutils-0.13_1 depends on package: py311-argh>=0.26.2 - found
===>   Returning to build of py311-gffutils-0.13_1
===>   py311-gffutils-0.13_1 depends on package: py311-pyfaidx>=0.5.5.2 - not found
===>   Installing existing package /packages/All/py311-pyfaidx-0.5.9.5_1.pkg
[13amd64-weekly-desktop-job-02] Installing py311-pyfaidx-0.5.9.5_1...
[13amd64-weekly-desktop-job-02] `-- Installing py311-six-1.17.0...
[13amd64-weekly-desktop-job-02] `-- Extracting py311-six-1.17.0: ........ done
[13amd64-weekly-desktop-job-02] Extracting py311-pyfaidx-0.5.9.5_1: .......... done
===>   py311-gffutils-0.13_1 depends on package: py311-pyfaidx>=0.5.5.2 - found
===>   Returning to build of py311-gffutils-0.13_1
===>   py311-gffutils-0.13_1 depends on package: py311-simplejson>0 - not found
===>   Installing existing package /packages/All/py311-simplejson-3.18.4_1.pkg
[13amd64-weekly-desktop-job-02] Installing py311-simplejson-3.18.4_1...
[13amd64-weekly-desktop-job-02] Extracting py311-simplejson-3.18.4_1: .......... done
===>   py311-gffutils-0.13_1 depends on package: py311-simplejson>0 - found
===>   Returning to build of py311-gffutils-0.13_1
===>   py311-gffutils-0.13_1 depends on package: py311-six>=1.12.0 - found
===>   py311-gffutils-0.13_1 depends on file: /usr/local/bin/python3.11 - found
===========================================================================
=======================<phase: stage          >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  Staging for py311-gffutils-0.13_1
===>   Generating temporary packing list
/usr/local/lib/python3.11/site-packages/setuptools/dist.py:530: UserWarning: Normalizing ' 0.13' to '0.13'
  warnings.warn(tmpl.format(**locals()))
running install
/usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running build
running build_py
running build_scripts
running install_lib
creating /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11
creating /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages
creating /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/attributes.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/helpers.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/gffwriter.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/pybedtools_integration.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/iterators.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/__init__.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/interface.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/version.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/inspect.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/feature.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/merge_criteria.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/bins.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/constants.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/biopython_integration.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/parser.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/exceptions.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
copying build/lib/gffutils/convert.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
creating /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/test_merge.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/test_1.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/conftest.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/helpers_test.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/__init__.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/feature_test.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/test_cli.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/test_issues.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/test_biopython_integration.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/synth_test_base.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/parser_test.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/test_merge_all.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/attr_test_cases.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/test_iterators.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
copying build/lib/gffutils/test/performance_evaluation.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
creating /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/keep-order-test.gtf -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/gff_example1.gff3 -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/gff_example1.gff3.gz -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/synthetic.gff3 -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/gencode-v19.gtf -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/dm6-chr2L.fa.fai -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/sharr.gtf -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/F3-unique-3.v2.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/jgi_gff2.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/gms2_example.gff3 -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/dm6-chr2L.fa -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/issue167.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/wormbase_gff2_alt.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/keyval_sep_in_attrs.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/issue_197.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/intro_docs_example.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/mouse_extra_comma.gff3 -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/FBgn0031208.gtf.db -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/nonascii -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/FBgn0031208.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/download-large-annotation-files.sh -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/ncbi_gff3.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/gencode.vM8.chromsizes.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/ensembl_gtf.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/hybrid1.gff3 -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/FBgn0031208.gtf -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/wormbase_gff2.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/random-chr.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/glimmer_nokeyval.gff3 -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/issue174.gtf -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/unsanitized.gff -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/data
copying build/lib/gffutils/test/expected.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test
creating /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/scripts
copying build/lib/gffutils/scripts/gffutils-flybase-convert.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/scripts
copying build/lib/gffutils/create.py -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/attributes.py to attributes.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/helpers.py to helpers.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/gffwriter.py to gffwriter.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/pybedtools_integration.py to pybedtools_integration.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/iterators.py to iterators.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/__init__.py to __init__.cpython-311.pyc
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byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/inspect.py to inspect.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/feature.py to feature.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/merge_criteria.py to merge_criteria.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/bins.py to bins.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/constants.py to constants.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/biopython_integration.py to biopython_integration.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/parser.py to parser.cpython-311.pyc
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byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/test_merge.py to test_merge.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/test_1.py to test_1.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/conftest.py to conftest.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/helpers_test.py to helpers_test.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/__init__.py to __init__.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/feature_test.py to feature_test.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/test_cli.py to test_cli.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/test_issues.py to test_issues.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/test_biopython_integration.py to test_biopython_integration.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/synth_test_base.py to synth_test_base.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/parser_test.py to parser_test.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/test_merge_all.py to test_merge_all.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/attr_test_cases.py to attr_test_cases.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/test_iterators.py to test_iterators.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/performance_evaluation.py to performance_evaluation.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/test/expected.py to expected.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/scripts/gffutils-flybase-convert.py to gffutils-flybase-convert.cpython-311.pyc
byte-compiling /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils/create.py to create.cpython-311.pyc
writing byte-compilation script '/tmp/tmpd00dnsby.py'
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removing /tmp/tmpd00dnsby.py
running install_egg_info
running egg_info
writing gffutils.egg-info/PKG-INFO
writing dependency_links to gffutils.egg-info/dependency_links.txt
writing requirements to gffutils.egg-info/requires.txt
writing top-level names to gffutils.egg-info/top_level.txt
reading manifest file 'gffutils.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.rst' under directory 'docs/source'
warning: no files found matching '*.py' under directory 'docs/source'
warning: no files found matching '*' under directory 'docs/source/images'
warning: no files found matching 'docs/Makefile'
warning: no files found matching 'docs/make.bat'
warning: no files found matching 'gffutils/test/data/__init__.py'
warning: no files found matching 'gffutils/test/data/t.py'
adding license file 'LICENSE'
writing manifest file 'gffutils.egg-info/SOURCES.txt'
Copying gffutils.egg-info to /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/lib/python3.11/site-packages/gffutils-0.13-py3.11.egg-info
running install_scripts
copying build/scripts-3.11/gffutils-cli -> /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/bin
changing mode of /wrkdirs/usr/ports/biology/py-gffutils/work-py311/stage/usr/local/bin/gffutils-cli to 755
writing list of installed files to '/wrkdirs/usr/ports/biology/py-gffutils/work-py311/.PLIST.pymodtmp'
===> Creating unique files: Move MAN files needing SUFFIX
===> Creating unique files: Move files needing SUFFIX
Move: bin/gffutils-cli --> bin/gffutils-cli-3.11
Link: @bin/gffutils-cli --> bin/gffutils-cli-3.11
====> Compressing man pages (compress-man)
===========================================================================
=======================<phase: package        >============================
===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-04T21:16:30+0000' 'PKG_NOTE_ports_top_git_hash=57a50b106b87' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=06a08e69f3ac' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  Building packages for py311-gffutils-0.13_1
===>   Building py311-gffutils-0.13_1
===========================================================================
=>> Cleaning up wrkdir
===>  Cleaning for py311-gffutils-0.13_1
build of biology/py-gffutils@py311 | py311-gffutils-0.13_1 ended at Sun May  4 17:16:45 EDT 2025
build time: 00:00:16