------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.7.txz ===== Message from python37-3.7.7: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/py37-setuptools-44.0.0.txz Installing /packages/All/py37-toml-0.10.0.txz Installing /packages/All/py37-setuptools_scm-3.4.3.txz Installing /packages/All/py37-cython-0.29.15.txz Installing /packages/All/py37-bz2file-0.98.txz Installing /packages/All/zopfli-1.0.3_1.txz Installing /packages/All/pigz-2.4.txz Installing /packages/All/py37-xopen-0.8.4.txz Installing /packages/All/py37-dnaio-0.4.1.txz SUCCEEDED 00:00:08 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py37-cutadapt-2.7 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py37-cutadapt-2.7 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-cutadapt-2.7 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py37-cutadapt-2.7 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-cutadapt-2.7 for building => SHA256 Checksum OK for cutadapt-2.7.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py37-cutadapt-2.7 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-cutadapt-2.7 for building ===> Extracting for py37-cutadapt-2.7 => SHA256 Checksum OK for cutadapt-2.7.tar.gz. Extracted Memory Use: 2.01M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py37-cutadapt-2.7 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py37-cutadapt-2.7 depends on package: py37-setuptools_scm>0 - found ===> py37-cutadapt-2.7 depends on executable: cython-3.7 - found ===> py37-cutadapt-2.7 depends on package: py37-setuptools>0 - found ===> py37-cutadapt-2.7 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py37-cutadapt-2.7 depends on package: py37-setuptools_scm>0 - found ===> py37-cutadapt-2.7 depends on executable: cython-3.7 - found ===> py37-cutadapt-2.7 depends on package: py37-setuptools>0 - found ===> py37-cutadapt-2.7 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for py37-cutadapt-2.7 running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py37-cutadapt-2.7 running build running build_py creating build creating build/lib.dragonfly-5.9-x86_64-3.7 creating build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/utils.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/filters.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/adapters.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/align.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/modifiers.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/log.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/report.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/pipeline.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/_version.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/parser.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt copying src/cutadapt/__main__.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt running build_ext building 'cutadapt._align' extension creating build/temp.dragonfly-5.9-x86_64-3.7 creating build/temp.dragonfly-5.9-x86_64-3.7/src creating build/temp.dragonfly-5.9-x86_64-3.7/src/cutadapt cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -c src/cutadapt/_align.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/cutadapt/_align.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/src/cutadapt/_align.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/_align.so building 'cutadapt.qualtrim' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -c src/cutadapt/qualtrim.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/cutadapt/qualtrim.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/src/cutadapt/qualtrim.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/qualtrim.so SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py37-cutadapt-2.7 depends on package: py37-xopen>=0.8.4 - found ===> py37-cutadapt-2.7 depends on package: py37-dnaio>=0.4.1 - found ===> py37-cutadapt-2.7 depends on package: py37-setuptools>0 - found ===> py37-cutadapt-2.7 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py37-cutadapt-2.7 ===> py37-cutadapt-2.7 depends on package: py37-xopen>=0.8.4 - found ===> py37-cutadapt-2.7 depends on package: py37-dnaio>=0.4.1 - found ===> py37-cutadapt-2.7 depends on package: py37-setuptools>0 - found ===> py37-cutadapt-2.7 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list running install running build running build_py copying src/cutadapt/_version.py -> build/lib.dragonfly-5.9-x86_64-3.7/cutadapt running build_ext running install_lib creating /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7 creating /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages creating /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/_align.so -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/qualtrim.so -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/pipeline.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/__init__.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/modifiers.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/parser.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/report.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/_version.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/log.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/utils.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/__main__.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/align.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/adapters.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt copying build/lib.dragonfly-5.9-x86_64-3.7/cutadapt/filters.py -> /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/pipeline.py to pipeline.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/modifiers.py to modifiers.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/parser.py to parser.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/report.py to report.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/_version.py to _version.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/log.py to log.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/utils.py to utils.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/__main__.py to __main__.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/align.py to align.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/adapters.py to adapters.cpython-37.pyc byte-compiling /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt/filters.py to filters.cpython-37.pyc writing byte-compilation script '/tmp/tmpso0u6cz0.py' /usr/local/bin/python3.7 /tmp/tmpso0u6cz0.py removing /tmp/tmpso0u6cz0.py running install_egg_info running egg_info creating src/cutadapt.egg-info writing src/cutadapt.egg-info/PKG-INFO writing dependency_links to src/cutadapt.egg-info/dependency_links.txt writing entry points to src/cutadapt.egg-info/entry_points.txt writing requirements to src/cutadapt.egg-info/requires.txt writing top-level names to src/cutadapt.egg-info/top_level.txt writing manifest file 'src/cutadapt.egg-info/SOURCES.txt' reading manifest file 'src/cutadapt.egg-info/SOURCES.txt' writing manifest file 'src/cutadapt.egg-info/SOURCES.txt' Copying src/cutadapt.egg-info to /construction/biology/py-cutadapt/stage/usr/local/lib/python3.7/site-packages/cutadapt-2.7-py3.7.egg-info running install_scripts Installing cutadapt script to /construction/biology/py-cutadapt/stage/usr/local/bin writing list of installed files to '/construction/biology/py-cutadapt/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/cutadapt --> bin/cutadapt-3.7 Link: @bin/cutadapt --> bin/cutadapt-3.7 ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.7/site-packages/cutadapt/_align.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py37-cutadapt-2.7 file sizes/checksums [46]: 0% file sizes/checksums [46]: 100% packing files [46]: 0% packing files [46]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:28