------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210116.txz Installing /packages/All/readline-8.0.4_1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/openssl-1.1.1i,1.txz Installing /packages/All/python37-3.7.9_1.txz ===== Message from python37-3.7.9_1: -- 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-cython-0.29.21.txz SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py37-hits-0.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py37-hits-0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-hits-0.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py37-hits-0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-hits-0.1 for building => SHA256 Checksum OK for hits-0.1.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py37-hits-0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-hits-0.1 for building ===> Extracting for py37-hits-0.1 => SHA256 Checksum OK for hits-0.1.tar.gz. Extracted Memory Use: 3.18M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py37-hits-0.1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py37-hits-0.1 depends on executable: cython-3.7 - found ===> py37-hits-0.1 depends on package: py37-setuptools>0 - found ===> py37-hits-0.1 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py37-hits-0.1 depends on executable: cython-3.7 - found ===> py37-hits-0.1 depends on package: py37-setuptools>0 - found ===> py37-hits-0.1 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for py37-hits-0.1 running config SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py37-hits-0.1 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/hits copying hits/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/sam.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/mapping_tools.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/paired_end.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/fastq.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/sw.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/genetic_code.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/annotation.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/utilities.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/external_sort.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/fasta.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/interval.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/visualize_structure.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/intensities_illumina.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/ipython.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/gff.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/variants.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/bus.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/adapters.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits copying hits/genomes.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits creating build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize copying hits/visualize/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize copying hits/visualize/fastq.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize copying hits/visualize/gels.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize copying hits/visualize/define_igv_colors.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize creating build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/external_coffeescript.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/pc.py -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_two_level_menu.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_color.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/pc_box_select.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/screen_menu.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_search.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_selection.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_label_button.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_cluster_button.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/screen_range.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_heatmap.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_grid.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/screen_search.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/pc_selection.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/screen_scatter_selection.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_menu.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_size_menu.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_annotation_button.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_label.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/pc_hover.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_save_button.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/pc_search.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_range.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_size.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_alpha.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/screen_errorbars_button.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/screen_significance_filter.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_case_sensitive.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_subset_menu.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/scatter_zoom_to_data.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/pc_clear.coffee -> build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive copying hits/visualize/interactive/example_df.txt -> build/lib.dragonfly-5.9-x86_64-3.7/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-5.9-x86_64-3.7 creating build/temp.dragonfly-5.9-x86_64-3.7/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/python3.7m -c hits/adapters_cython.c -o build/temp.dragonfly-5.9-x86_64-3.7/hits/adapters_cython.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/hits/adapters_cython.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/hits/adapters_cython.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/python3.7m -c hits/fastq_cython.c -o build/temp.dragonfly-5.9-x86_64-3.7/hits/fastq_cython.o hits/fastq_cython.c: In function '__pyx_pf_12fastq_cython_2process_read': hits/fastq_cython.c:2638:29: 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:2912:29: 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-5.9-x86_64-3.7/hits/fastq_cython.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/hits/fastq_cython.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/python3.7m -c hits/sw_cython.c -o build/temp.dragonfly-5.9-x86_64-3.7/hits/sw_cython.o hits/sw_cython.c: In function '__pyx_pf_9sw_cython_4extend_perfect_seed': hits/sw_cython.c:4873:37: 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:4880:38: 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:5195:37: 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:5202:38: 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-5.9-x86_64-3.7/hits/sw_cython.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/hits/sw_cython.so SUCCEEDED 00:00:20 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py37-hits-0.1 depends on package: py37-setuptools>0 - found ===> py37-hits-0.1 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py37-hits-0.1 ===> py37-hits-0.1 depends on package: py37-setuptools>0 - found ===> py37-hits-0.1 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list running install 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/python3.7 creating /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages creating /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/sw_cython.so -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/gff.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/bus.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/interval.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/sam.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/genetic_code.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/__init__.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/mapping_tools.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits creating /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/gels.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/__init__.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/fastq.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize creating /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/screen_scatter_selection.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/__init__.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_heatmap.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_range.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_two_level_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_color.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_label.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_alpha.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/external_coffeescript.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/screen_search.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/pc_selection.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/screen_errorbars_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/pc_clear.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_size_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/example_df.txt -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_subset_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_annotation_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_search.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/pc.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/pc_search.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_grid.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_save_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/screen_range.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_selection.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_case_sensitive.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/pc_hover.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_cluster_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_size.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/screen_menu.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_label_button.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/scatter_zoom_to_data.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/pc_box_select.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/interactive/screen_significance_filter.coffee -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize/define_igv_colors.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize copying build/lib.dragonfly-5.9-x86_64-3.7/hits/variants.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/fasta.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/intensities_illumina.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/ipython.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/annotation.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/adapters_cython.so -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/sw.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/external_sort.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/genomes.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/fastq.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/paired_end.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/adapters.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/visualize_structure.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/utilities.py -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits copying build/lib.dragonfly-5.9-x86_64-3.7/hits/fastq_cython.so -> /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/gff.py to gff.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/bus.py to bus.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/interval.py to interval.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/sam.py to sam.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/genetic_code.py to genetic_code.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/mapping_tools.py to mapping_tools.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/gels.py to gels.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/fastq.py to fastq.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive/external_coffeescript.py to external_coffeescript.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/interactive/pc.py to pc.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize/define_igv_colors.py to define_igv_colors.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/variants.py to variants.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/fasta.py to fasta.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/intensities_illumina.py to intensities_illumina.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/ipython.py to ipython.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/annotation.py to annotation.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/sw.py to sw.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/external_sort.py to external_sort.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/genomes.py to genomes.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/fastq.py to fastq.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/paired_end.py to paired_end.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/adapters.py to adapters.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/visualize_structure.py to visualize_structure.cpython-37.pyc byte-compiling /construction/biology/py-hits/stage/usr/local/lib/python3.7/site-packages/hits/utilities.py to utilities.cpython-37.pyc writing byte-compilation script '/tmp/tmpvbqtub62.py' /usr/local/bin/python3.7 /tmp/tmpvbqtub62.py removing /tmp/tmpvbqtub62.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/python3.7/site-packages/hits-0.1-py3.7.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) Error: /usr/local/lib/python3.7/site-packages/hits/adapters_cython.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: 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 py37-hits-0.1 file sizes/checksums [120]: 0% file sizes/checksums [120]: 83% file sizes/checksums [120]: 100% packing files [120]: 0% packing files [120]: 83% packing files [120]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:04 TOTAL TIME 00:00:37