------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/biology/py-hits XDG_CONFIG_HOME=/construction/biology/py-hits XDG_CACHE_HOME=/construction/biology/py-hits/.cache HOME=/construction/biology/py-hits TMPDIR="/tmp" PATH=/construction/biology/py-hits/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-hits/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-hits XDG_CONFIG_HOME=/construction/biology/py-hits XDG_CACHE_HOME=/construction/biology/py-hits/.cache HOME=/construction/biology/py-hits TMPDIR="/tmp" PATH=/construction/biology/py-hits/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-hits/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/py-hits/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/hits" EXAMPLESDIR="share/examples/hits" DATADIR="share/hits" WWWDIR="www/hits" ETCDIR="etc/hits" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hits DOCSDIR=/usr/local/share/doc/hits EXAMPLESDIR=/usr/local/share/examples/hits WWWDIR=/usr/local/www/hits ETCDIR=/usr/local/etc/hits SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/py39-setuptools-63.1.0_1.pkg Installing /packages/All/py39-cython-0.29.35.pkg Installing /packages/All/ccache-3.7.12_4.pkg Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-hits-0.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-hits-0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-hits-0.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-hits-0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-hits-0.1 for building => SHA256 Checksum OK for hits-0.1.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-hits-0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-hits-0.1 for building ===> Extracting for py39-hits-0.1 => SHA256 Checksum OK for hits-0.1.tar.gz. Extracted Memory Use: 3.18M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-hits-0.1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-hits-0.1 depends on executable: cython-3.9 - found ===> py39-hits-0.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-hits-0.1 depends on file: /usr/local/bin/python3.9 - found ===> py39-hits-0.1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-hits-0.1 depends on executable: cython-3.9 - found ===> py39-hits-0.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-hits-0.1 depends on file: /usr/local/bin/python3.9 - found ===> py39-hits-0.1 depends on file: /usr/local/bin/ccache - found ===> Configuring for py39-hits-0.1 running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-hits-0.1 running build running build_py creating build creating build/lib.dragonfly-6.5-x86_64-cpython-39 creating build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/intensities_illumina.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/external_sort.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/genetic_code.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/fasta.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/ipython.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/mapping_tools.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/genomes.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/variants.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/sam.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/fastq.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/sw.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/annotation.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/interval.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/visualize_structure.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/utilities.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/adapters.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/bus.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/paired_end.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits copying hits/gff.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits creating build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize copying hits/visualize/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize copying hits/visualize/define_igv_colors.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize copying hits/visualize/fastq.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize copying hits/visualize/gels.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize creating build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/pc.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/external_coffeescript.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_case_sensitive.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_grid.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_size_menu.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/screen_errorbars_button.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/pc_hover.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_label.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/screen_significance_filter.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_zoom_to_data.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_annotation_button.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_size.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_color.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_alpha.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_search.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_save_button.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/pc_search.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_selection.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/screen_menu.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_heatmap.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/pc_box_select.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/screen_scatter_selection.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_range.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/pc_selection.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/screen_search.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_two_level_menu.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/pc_clear.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/screen_range.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_menu.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_label_button.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_cluster_button.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/scatter_subset_menu.coffee -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive copying hits/visualize/interactive/example_df.txt -> build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive running build_ext cythoning hits/adapters_cython.pyx to hits/adapters_cython.c cythoning hits/fastq_cython.pyx to hits/fastq_cython.c cythoning hits/sw_cython.pyx to hits/sw_cython.c building 'adapters_cython' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39 creating build/temp.dragonfly-6.5-x86_64-cpython-39/hits 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/python3.9 -c hits/adapters_cython.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/hits/adapters_cython.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/hits/adapters_cython.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/hits/adapters_cython.cpython-39.so building 'fastq_cython' 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/python3.9 -c hits/fastq_cython.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/hits/fastq_cython.o hits/fastq_cython.c: In function '__pyx_pf_12fastq_cython_2process_read': hits/fastq_cython.c:2805:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] __pyx_t_6 = ((__pyx_v_q >= __pyx_v_min_q) != 0); ^~ hits/fastq_cython.c: In function '__pyx_pf_12fastq_cython_4process_Alignment': hits/fastq_cython.c:3079:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] __pyx_t_6 = ((__pyx_v_q >= __pyx_v_min_q) != 0); ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/hits/fastq_cython.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/hits/fastq_cython.cpython-39.so building 'sw_cython' 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/python3.9 -c hits/sw_cython.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/hits/sw_cython.o hits/sw_cython.c: In function '__pyx_pf_9sw_cython_4extend_perfect_seed': hits/sw_cython.c:5026:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_2 = ((__pyx_v_query_end < __pyx_t_3) != 0); ^ hits/sw_cython.c:5033:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_2 = ((__pyx_v_target_end < __pyx_t_3) != 0); ^ hits/sw_cython.c: In function '__pyx_pf_9sw_cython_6extend_perfect_seed_with_one_nt_deletion': hits/sw_cython.c:5348:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_2 = ((__pyx_v_query_end < __pyx_t_4) != 0); ^ hits/sw_cython.c:5355:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] __pyx_t_2 = ((__pyx_v_target_end < __pyx_t_4) != 0); ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/hits/sw_cython.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/hits/sw_cython.cpython-39.so SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-hits-0.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-hits-0.1 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-hits-0.1 ===> py39-hits-0.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-hits-0.1 depends on file: /usr/local/bin/python3.9 - found ===> Generating temporary packing list running install /usr/local/lib/python3.9/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_ext skipping 'hits/adapters_cython.c' Cython extension (up-to-date) skipping 'hits/fastq_cython.c' Cython extension (up-to-date) skipping 'hits/sw_cython.c' Cython extension (up-to-date) running install_lib creating /construction/biology/py-hits/stage/usr/local/lib/python3.9 creating /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages creating /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/intensities_illumina.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/external_sort.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/genetic_code.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/fasta.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/ipython.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/mapping_tools.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/genomes.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/__init__.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/variants.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/sam.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/fastq.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/sw.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/annotation.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/interval.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize_structure.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/utilities.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/adapters.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/bus.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/paired_end.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/gff.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits creating /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/__init__.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/define_igv_colors.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/fastq.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/gels.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize creating /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/__init__.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/pc.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/external_coffeescript.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_case_sensitive.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_grid.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_size_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/screen_errorbars_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/pc_hover.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_label.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/screen_significance_filter.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_zoom_to_data.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_annotation_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_size.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_color.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_alpha.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_search.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_save_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/pc_search.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_selection.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/screen_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_heatmap.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/pc_box_select.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/screen_scatter_selection.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_range.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/pc_selection.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/screen_search.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_two_level_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/pc_clear.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/screen_range.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_label_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_cluster_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/scatter_subset_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/visualize/interactive/example_df.txt -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/sw_cython.cpython-39.so -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/fastq_cython.cpython-39.so -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits copying build/lib.dragonfly-6.5-x86_64-cpython-39/hits/adapters_cython.cpython-39.so -> /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/intensities_illumina.py to intensities_illumina.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/external_sort.py to external_sort.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/genetic_code.py to genetic_code.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/fasta.py to fasta.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/ipython.py to ipython.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/mapping_tools.py to mapping_tools.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/genomes.py to genomes.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/variants.py to variants.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/sam.py to sam.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/fastq.py to fastq.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/sw.py to sw.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/annotation.py to annotation.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/interval.py to interval.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize_structure.py to visualize_structure.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/utilities.py to utilities.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/adapters.py to adapters.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/bus.py to bus.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/paired_end.py to paired_end.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/gff.py to gff.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/define_igv_colors.py to define_igv_colors.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/fastq.py to fastq.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/gels.py to gels.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive/pc.py to pc.cpython-39.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits/visualize/interactive/external_coffeescript.py to external_coffeescript.cpython-39.pyc writing byte-compilation script '/tmp/tmp30hmxogy.py' /usr/local/bin/python3.9 /tmp/tmp30hmxogy.py removing /tmp/tmp30hmxogy.py running install_egg_info running egg_info writing hits.egg-info/PKG-INFO writing dependency_links to hits.egg-info/dependency_links.txt writing requirements to hits.egg-info/requires.txt writing top-level names to hits.egg-info/top_level.txt reading manifest file 'hits.egg-info/SOURCES.txt' writing manifest file 'hits.egg-info/SOURCES.txt' Copying hits.egg-info to /construction/biology/py-hits/stage/usr/local/lib/python3.9/site-packages/hits-0.1-py3.9.egg-info running install_scripts writing list of installed files to '/construction/biology/py-hits/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-hits-0.1 file sizes/checksums [120]: 0% file sizes/checksums [120]: 83% file sizes/checksums [120]: 100% Service unavailablepacking files [120]: 0% packing files [120]: 83% packing files [120]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:38