------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/metis-5.1.0_8.txz ===== Message from metis-5.1.0_8: -- ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/tbb-2020.3.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/binutils-2.33.1_3,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.10,1.txz Installing /packages/All/suitesparse-5.8.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.9.txz ===== Message from python37-3.7.9: -- 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-numpy-1.16.6,1.txz Installing /packages/All/py37-six-1.15.0.txz Installing /packages/All/py37-cython-0.29.15.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:01:05 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py37-bx-python-0.8.9 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py37-bx-python-0.8.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-bx-python-0.8.9 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py37-bx-python-0.8.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-bx-python-0.8.9 for building => SHA256 Checksum OK for bxlab-bx-python-v0.8.9_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py37-bx-python-0.8.9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-bx-python-0.8.9 for building ===> Extracting for py37-bx-python-0.8.9 => SHA256 Checksum OK for bxlab-bx-python-v0.8.9_GH0.tar.gz. Extracted Memory Use: 4.12M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py37-bx-python-0.8.9 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py37-bx-python-0.8.9 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-bx-python-0.8.9 depends on package: py37-six>0 - found ===> py37-bx-python-0.8.9 depends on executable: cython-3.7 - found ===> py37-bx-python-0.8.9 depends on package: py37-setuptools>0 - found ===> py37-bx-python-0.8.9 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py37-bx-python-0.8.9 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-bx-python-0.8.9 depends on package: py37-six>0 - found ===> py37-bx-python-0.8.9 depends on executable: cython-3.7 - found ===> py37-bx-python-0.8.9 depends on package: py37-setuptools>0 - found ===> py37-bx-python-0.8.9 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for py37-bx-python-0.8.9 running config SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py37-bx-python-0.8.9 running build running build_py creating build creating build/lib.dragonfly-5.9-x86_64-3.7 copying lib/psyco_full.py -> build/lib.dragonfly-5.9-x86_64-3.7 creating build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/binned_array.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/binned_array_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/bitset_builders.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/bitset_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/bitset_utils.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/filter.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/gene_reader.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/interval_index_file.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/interval_index_file_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/seqmapping.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/seqmapping_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/wiggle.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx copying lib/bx/wiggle_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx creating build/lib.dragonfly-5.9-x86_64-3.7/bx_extras copying lib/bx_extras/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx_extras copying lib/bx_extras/fpconst.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx_extras copying lib/bx_extras/fpconst_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx_extras copying lib/bx_extras/lrucache.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx_extras copying lib/bx_extras/pstat.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx_extras copying lib/bx_extras/pyparsing.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx_extras copying lib/bx_extras/stats.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx_extras creating build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/score_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/score.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/maf_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/axt.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/core.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/epo.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/epo_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/lav.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/lav_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align copying lib/bx/align/maf.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align creating build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays copying lib/bx/arrays/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays copying lib/bx/arrays/array_tree_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays creating build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi copying lib/bx/bbi/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi copying lib/bx/bbi/bigwig_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi creating build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook copying lib/bx/cookbook/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook copying lib/bx/cookbook/argparse.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook copying lib/bx/cookbook/attribute.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook copying lib/bx/cookbook/doc_optparse.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook copying lib/bx/cookbook/progress_bar.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook creating build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals copying lib/bx/intervals/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals copying lib/bx/intervals/cluster_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals copying lib/bx/intervals/intersection_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals copying lib/bx/intervals/io.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals copying lib/bx/intervals/random_intervals.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals creating build/lib.dragonfly-5.9-x86_64-3.7/bx/intseq copying lib/bx/intseq/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intseq creating build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/bgzf_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/binary_file.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/cdb.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/cdb_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/filecache.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/filecache_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/readlengths.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/seekbzip2.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/seekbzip2_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/seeklzop.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc copying lib/bx/misc/seeklzop_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/misc creating build/lib.dragonfly-5.9-x86_64-3.7/bx/motif copying lib/bx/motif/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif copying lib/bx/motif/pwm.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif copying lib/bx/motif/pwm_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif creating build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo copying lib/bx/phylo/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo copying lib/bx/phylo/newick.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo copying lib/bx/phylo/newick_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo copying lib/bx/phylo/phast.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo copying lib/bx/phylo/phast_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo creating build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/maf_select_motifs.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/position_weight_matrix.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/pwm_score_maf.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/pwm_score_positions.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm copying lib/bx/pwm/pwm_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm creating build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/core.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/fasta.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/fasta_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/nib.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/nib_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/qdna.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/qdna_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/seq.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/seq_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/twobit.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq copying lib/bx/seq/twobit_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/seq creating build/lib.dragonfly-5.9-x86_64-3.7/bx/tabular copying lib/bx/tabular/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/tabular copying lib/bx/tabular/io.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/tabular creating build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask copying lib/bx/align/sitemask/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask copying lib/bx/align/sitemask/core.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask copying lib/bx/align/sitemask/cpg.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask copying lib/bx/align/sitemask/quality.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask creating build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools copying lib/bx/align/tools/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools copying lib/bx/align/tools/chop.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools copying lib/bx/align/tools/fuse.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools copying lib/bx/align/tools/thread.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools copying lib/bx/align/tools/tile.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools creating build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/base_coverage.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/complement.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/concat.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/coverage.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/find_clusters.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/intersect.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/join.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/merge.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/quicksect.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations copying lib/bx/intervals/operations/subtract.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations creating build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/io copying lib/bx/motif/io/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/io copying lib/bx/motif/io/transfac.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/io copying lib/bx/motif/io/transfac_tests.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/io creating build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/logo copying lib/bx/motif/logo/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/logo copying lib/bx/motif/logo/template.ps -> build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/logo Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext cythoning lib/bx/bitset.pyx to lib/bx/bitset.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/bitset.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/intervals/intersection.pyx to lib/bx/intervals/intersection.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/intervals/intersection.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/align/_core.pyx to lib/bx/align/_core.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/align/_core.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/seq/_nib.pyx to lib/bx/seq/_nib.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/seq/_nib.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/seq/_twobit.pyx to lib/bx/seq/_twobit.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/seq/_twobit.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/_seqmapping.pyx to lib/bx/_seqmapping.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/_seqmapping.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/misc/bgzf.pyx to lib/bx/misc/bgzf.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/misc/bgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/intervals/cluster.pyx to lib/bx/intervals/cluster.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/intervals/cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/pwm/_position_weight_matrix.pyx to lib/bx/pwm/_position_weight_matrix.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/pwm/_position_weight_matrix.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/motif/_pwm.pyx to lib/bx/motif/_pwm.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/motif/_pwm.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/arrays/array_tree.pyx to lib/bx/arrays/array_tree.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/arrays/array_tree.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/bbi/bpt_file.pyx to lib/bx/bbi/bpt_file.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/bbi/bpt_file.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/bbi/cirtree_file.pyx to lib/bx/bbi/cirtree_file.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/bbi/cirtree_file.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/bbi/bbi_file.pyx to lib/bx/bbi/bbi_file.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/bbi/bbi_file.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/bbi/bigwig_file.pyx to lib/bx/bbi/bigwig_file.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/bbi/bigwig_file.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/bbi/bigbed_file.pyx to lib/bx/bbi/bigbed_file.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/bbi/bigbed_file.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/align/_epo.pyx to lib/bx/align/_epo.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/align/_epo.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/arrays/bed.pyx to lib/bx/arrays/bed.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/arrays/bed.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/arrays/wiggle.pyx to lib/bx/arrays/wiggle.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/arrays/wiggle.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: lib/bx/arrays/wiggle.pyx:94:20: Unreachable code cythoning lib/bx/align/sitemask/_cpg.pyx to lib/bx/align/sitemask/_cpg.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/align/sitemask/_cpg.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/intseq/ngramcount.pyx to lib/bx/intseq/ngramcount.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/intseq/ngramcount.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning lib/bx/misc/_seekbzip2.pyx to lib/bx/misc/_seekbzip2.c /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/py-bx-python/bx-python-0.8.9/lib/bx/misc/_seekbzip2.pyx tree = Parsing.p_module(s, pxd, full_module_name) building 'bx.bitset' extension creating build/temp.dragonfly-5.9-x86_64-3.7 creating build/temp.dragonfly-5.9-x86_64-3.7/lib creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx creating build/temp.dragonfly-5.9-x86_64-3.7/src creating build/temp.dragonfly-5.9-x86_64-3.7/src/kent 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 -Isrc/kent -Isrc -I/usr/local/include/python3.7m -c lib/bx/bitset.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bitset.o 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 -Isrc/kent -Isrc -I/usr/local/include/python3.7m -c src/binBits.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/binBits.o 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 -Isrc/kent -Isrc -I/usr/local/include/python3.7m -c src/kent/bits.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/kent/bits.o 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 -Isrc/kent -Isrc -I/usr/local/include/python3.7m -c src/kent/common.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/kent/common.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bitset.o build/temp.dragonfly-5.9-x86_64-3.7/src/binBits.o build/temp.dragonfly-5.9-x86_64-3.7/src/kent/bits.o build/temp.dragonfly-5.9-x86_64-3.7/src/kent/common.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/bitset.so building 'bx.intervals.intersection' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intervals 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 lib/bx/intervals/intersection.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intervals/intersection.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intervals/intersection.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/intersection.so building 'bx.align._core' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align 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 lib/bx/align/_core.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/_core.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/_core.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/align/_core.so building 'bx.seq._nib' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/seq 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 lib/bx/seq/_nib.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/seq/_nib.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/seq/_nib.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/_nib.so building 'bx.seq._twobit' 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 lib/bx/seq/_twobit.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/seq/_twobit.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/seq/_twobit.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/_twobit.so building 'bx._seqmapping' 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 lib/bx/_seqmapping.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/_seqmapping.o lib/bx/_seqmapping.c: In function '__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate': lib/bx/_seqmapping.c:1762:3: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 52, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.7m/Python.h:147, from lib/bx/_seqmapping.c:4: /usr/local/include/python3.7m/abstract.h:500:17: note: declared here PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~~ lib/bx/_seqmapping.c: In function '__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_8translate_list': lib/bx/_seqmapping.c:1962:3: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_7 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 75, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.7m/Python.h:147, from lib/bx/_seqmapping.c:4: /usr/local/include/python3.7m/abstract.h:500:17: note: declared here PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~~ lib/bx/_seqmapping.c: In function '__pyx_pf_2bx_11_seqmapping_15IntToIntMapping_6translate': lib/bx/_seqmapping.c:3007:3: warning: 'PyObject_AsReadBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsReadBuffer(__pyx_v_src, ((void const **)(&__pyx_v_s_buf)), (&__pyx_v_s_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 132, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.7m/Python.h:147, from lib/bx/_seqmapping.c:4: /usr/local/include/python3.7m/abstract.h:489:17: note: declared here PyAPI_FUNC(int) PyObject_AsReadBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~ lib/bx/_seqmapping.c:3108:3: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 137, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.7m/Python.h:147, from lib/bx/_seqmapping.c:4: /usr/local/include/python3.7m/abstract.h:500:17: note: declared here PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/_seqmapping.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/_seqmapping.so building 'bx.misc.bgzf' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/misc creating build/temp.dragonfly-5.9-x86_64-3.7/src/samtools 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 -Isrc/samtools -I/usr/local/include/python3.7m -c lib/bx/misc/bgzf.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/misc/bgzf.o 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 -Isrc/samtools -I/usr/local/include/python3.7m -c src/samtools/bgzf.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/samtools/bgzf.o src/samtools/bgzf.c: In function 'cache_block': src/samtools/bgzf.c:422:40: warning: comparison of integer expressions of different signedness: 'khint_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) { ^ src/samtools/bgzf.c: In function 'read_block': src/samtools/bgzf.c:462:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if (count != sizeof(header)) { ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/misc/bgzf.o build/temp.dragonfly-5.9-x86_64-3.7/src/samtools/bgzf.o -L/usr/local/lib -lz -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/bgzf.so building 'bx.intervals.cluster' 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 -Isrc -I/usr/local/include/python3.7m -c lib/bx/intervals/cluster.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intervals/cluster.o 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 -Isrc -I/usr/local/include/python3.7m -c src/cluster.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/cluster.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intervals/cluster.o build/temp.dragonfly-5.9-x86_64-3.7/src/cluster.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/cluster.so building 'bx.pwm._position_weight_matrix' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/pwm 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 -Isrc -I/usr/local/include/python3.7m -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/pwm/_position_weight_matrix.o 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 -Isrc -I/usr/local/include/python3.7m -c src/pwm_utils.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/pwm_utils.o src/pwm_utils.c: In function 'main': src/pwm_utils.c:11:27: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration] int string_size = strlen(argv[1]); ^~~~~~ src/pwm_utils.c:11:27: warning: incompatible implicit declaration of built-in function 'strlen' src/pwm_utils.c:11:27: note: include '' or provide a declaration of 'strlen' src/pwm_utils.c:5:1: +#include src/pwm_utils.c:11:27: int string_size = strlen(argv[1]); ^~~~~~ src/pwm_utils.c:12:29: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if (strlen(argv[2]) != string_size) { ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/pwm/_position_weight_matrix.o build/temp.dragonfly-5.9-x86_64-3.7/src/pwm_utils.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/_position_weight_matrix.so building 'bx.motif._pwm' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/motif 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/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c lib/bx/motif/_pwm.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/motif/_pwm.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/motif/_pwm.c:596: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/motif/_pwm.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/_pwm.so building 'bx.arrays.array_tree' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/arrays 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/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c lib/bx/arrays/array_tree.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/arrays/array_tree.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/arrays/array_tree.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/arrays/array_tree.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/array_tree.so building 'bx.bbi.bpt_file' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi 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 lib/bx/bbi/bpt_file.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bpt_file.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bpt_file.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bpt_file.so building 'bx.bbi.cirtree_file' 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 lib/bx/bbi/cirtree_file.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/cirtree_file.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/cirtree_file.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/cirtree_file.so building 'bx.bbi.bbi_file' 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/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c lib/bx/bbi/bbi_file.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bbi_file.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/bbi/bbi_file.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bbi_file.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bbi_file.so building 'bx.bbi.bigwig_file' 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/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c lib/bx/bbi/bigwig_file.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bigwig_file.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/bbi/bigwig_file.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ lib/bx/bbi/bigwig_file.c: In function '__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_block': lib/bx/bbi/bigwig_file.c:3275:30: warning: comparison of integer expressions of different signedness: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' {aka 'unsigned int'} [-Wsign-compare] __pyx_t_11 = ((__pyx_v_s < __pyx_v_self->start) != 0); ^ lib/bx/bbi/bigwig_file.c:3304:30: warning: comparison of integer expressions of different signedness: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' {aka 'unsigned int'} [-Wsign-compare] __pyx_t_11 = ((__pyx_v_e > __pyx_v_self->end) != 0); ^ lib/bx/bbi/bigwig_file.c: In function '__pyx_f_2bx_3bbi_11bigwig_file_29ArrayAccumulatingBlockHandler_handle_interval_value': lib/bx/bbi/bigwig_file.c:5183:76: warning: comparison of integer expressions of different signedness: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' {aka 'unsigned int'} [-Wsign-compare] for (__pyx_v_i = (__pyx_v_s - __pyx_v_self->__pyx_base.start); __pyx_v_i < __pyx_t_2; __pyx_v_i++) { ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bigwig_file.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bigwig_file.so building 'bx.bbi.bigbed_file' 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/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c lib/bx/bbi/bigbed_file.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bigbed_file.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/bbi/bigbed_file.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/bbi/bigbed_file.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bigbed_file.so building 'bx.align._epo' 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/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c lib/bx/align/_epo.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/_epo.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/align/_epo.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ lib/bx/align/_epo.c: In function '__pyx_f_2bx_5align_4_epo_bed_union': lib/bx/align/_epo.c:5390:237: warning: comparison of integer expressions of different signedness: '__pyx_t_5numpy_uint64_t' {aka 'long unsigned int'} and 'Py_ssize_t' {aka 'long int'} [-Wsign-compare] __pyx_t_4 = (((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_uint64_t *, __pyx_pybuffernd_elements.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_elements.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_elements.diminfo[1].strides)) <= __pyx_v_cen) != 0); ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/_epo.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/align/_epo.so building 'bx.arrays.bed' 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 lib/bx/arrays/bed.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/arrays/bed.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/arrays/bed.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/bed.so building 'bx.arrays.wiggle' 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 lib/bx/arrays/wiggle.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/arrays/wiggle.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/arrays/wiggle.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/wiggle.so building 'bx.align.sitemask._cpg' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/sitemask 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 lib/bx/align/sitemask/_cpg.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/sitemask/_cpg.o 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 lib/bx/align/sitemask/find_cpg.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/sitemask/find_cpg.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/sitemask/_cpg.o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/align/sitemask/find_cpg.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask/_cpg.so building 'bx.intseq.ngramcount' extension creating build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intseq 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 -Isrc -I/usr/local/include/python3.7m -c lib/bx/intseq/ngramcount.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intseq/ngramcount.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/intseq/ngramcount.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/intseq/ngramcount.so building 'bx.misc._seekbzip2' extension creating build/temp.dragonfly-5.9-x86_64-3.7/src/bunzip 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 -Isrc/bunzip -I/usr/local/include/python3.7m -c lib/bx/misc/_seekbzip2.c -o build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/misc/_seekbzip2.o 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 -Isrc/bunzip -I/usr/local/include/python3.7m -c src/bunzip/micro-bunzip.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/bunzip/micro-bunzip.o src/bunzip/micro-bunzip.c: In function 'get_bits': src/bunzip/micro-bunzip.c:99:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'char' [-Wsign-compare] while (bd->inbufBitCount dbufSize) return RETVAL_DATA_ERROR; ^ src/bunzip/micro-bunzip.c:298:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (bd->inbufBitCountmaxLen) { ^ src/bunzip/micro-bunzip.c:400:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(origPtr>=dbufCount) return RETVAL_DATA_ERROR; ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/lib/bx/misc/_seekbzip2.o build/temp.dragonfly-5.9-x86_64-3.7/src/bunzip/micro-bunzip.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/_seekbzip2.so running build_scripts creating build/scripts-3.7 copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.7 copying and adjusting scripts/align_print_template.py -> build/scripts-3.7 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.7 copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.7 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.7 copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.7 copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.7 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.7 copying and adjusting scripts/bed_complement.py -> build/scripts-3.7 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.7 copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.7 copying and adjusting scripts/bed_coverage.py -> build/scripts-3.7 copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.7 copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.7 copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.7 copying and adjusting scripts/bed_intersect.py -> build/scripts-3.7 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.7 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.7 copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.7 copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.7 copying and adjusting scripts/bnMapper.py -> build/scripts-3.7 copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.7 copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.7 copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.7 copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.7 copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.7 copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.7 copying and adjusting scripts/interval_join.py -> build/scripts-3.7 copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.7 copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.7 copying and adjusting scripts/line_select.py -> build/scripts-3.7 copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.7 copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.7 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.7 copying and adjusting scripts/maf_chop.py -> build/scripts-3.7 copying and adjusting scripts/maf_chunk.py -> build/scripts-3.7 copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.7 copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.7 copying and adjusting scripts/maf_count.py -> build/scripts-3.7 copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.7 copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.7 copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.7 copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.7 copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.7 copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.7 copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.7 copying and adjusting scripts/maf_filter.py -> build/scripts-3.7 copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.7 copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.7 copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.7 copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.7 copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.7 copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.7 copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.7 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.7 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.7 copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.7 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.7 copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.7 copying and adjusting scripts/maf_randomize.py -> build/scripts-3.7 copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.7 copying and adjusting scripts/maf_select.py -> build/scripts-3.7 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.7 copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.7 copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.7 copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.7 copying and adjusting scripts/maf_tile.py -> build/scripts-3.7 copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.7 copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.7 copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.7 copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.7 copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.7 copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.7 copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.7 copying and adjusting scripts/maf_truncate.py -> build/scripts-3.7 copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.7 copying and adjusting scripts/mask_quality.py -> build/scripts-3.7 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.7 copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.7 copying and adjusting scripts/nib_length.py -> build/scripts-3.7 copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.7 copying and adjusting scripts/out_to_chain.py -> build/scripts-3.7 copying and adjusting scripts/prefix_lines.py -> build/scripts-3.7 copying and adjusting scripts/pretty_table.py -> build/scripts-3.7 copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.7 copying and adjusting scripts/random_lines.py -> build/scripts-3.7 copying and adjusting scripts/table_add_column.py -> build/scripts-3.7 copying and adjusting scripts/table_filter.py -> build/scripts-3.7 copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.7 copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.7 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.7 copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.7 copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.7 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.7 changing mode of build/scripts-3.7/aggregate_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.7/align_print_template.py from 644 to 755 changing mode of build/scripts-3.7/axt_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.7/axt_to_fasta.py from 644 to 755 changing mode of build/scripts-3.7/axt_to_lav.py from 644 to 755 changing mode of build/scripts-3.7/axt_to_maf.py from 644 to 755 changing mode of build/scripts-3.7/bed_bigwig_profile.py from 644 to 755 changing mode of build/scripts-3.7/bed_build_windows.py from 644 to 755 changing mode of build/scripts-3.7/bed_complement.py from 644 to 755 changing mode of build/scripts-3.7/bed_count_by_interval.py from 644 to 755 changing mode of build/scripts-3.7/bed_count_overlapping.py from 644 to 755 changing mode of build/scripts-3.7/bed_coverage.py from 644 to 755 changing mode of build/scripts-3.7/bed_coverage_by_interval.py from 644 to 755 changing mode of build/scripts-3.7/bed_diff_basewise_summary.py from 644 to 755 changing mode of build/scripts-3.7/bed_extend_to.py from 644 to 755 changing mode of build/scripts-3.7/bed_intersect.py from 644 to 755 changing mode of build/scripts-3.7/bed_intersect_basewise.py from 644 to 755 changing mode of build/scripts-3.7/bed_merge_overlapping.py from 644 to 755 changing mode of build/scripts-3.7/bed_rand_intersect.py from 644 to 755 changing mode of build/scripts-3.7/bed_subtract_basewise.py from 644 to 755 changing mode of build/scripts-3.7/bnMapper.py from 644 to 755 changing mode of build/scripts-3.7/div_snp_table_chr.py from 644 to 755 changing mode of build/scripts-3.7/find_in_sorted_file.py from 644 to 755 changing mode of build/scripts-3.7/gene_fourfold_sites.py from 644 to 755 changing mode of build/scripts-3.7/get_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.7/int_seqs_to_char_strings.py from 644 to 755 changing mode of build/scripts-3.7/interval_count_intersections.py from 644 to 755 changing mode of build/scripts-3.7/interval_join.py from 644 to 755 changing mode of build/scripts-3.7/lav_to_axt.py from 644 to 755 changing mode of build/scripts-3.7/lav_to_maf.py from 644 to 755 changing mode of build/scripts-3.7/line_select.py from 644 to 755 changing mode of build/scripts-3.7/lzop_build_offset_table.py from 644 to 755 changing mode of build/scripts-3.7/mMK_bitset.py from 644 to 755 changing mode of build/scripts-3.7/maf_build_index.py from 644 to 755 changing mode of build/scripts-3.7/maf_chop.py from 644 to 755 changing mode of build/scripts-3.7/maf_chunk.py from 644 to 755 changing mode of build/scripts-3.7/maf_col_counts.py from 644 to 755 changing mode of build/scripts-3.7/maf_col_counts_all.py from 644 to 755 changing mode of build/scripts-3.7/maf_count.py from 644 to 755 changing mode of build/scripts-3.7/maf_covered_ranges.py from 644 to 755 changing mode of build/scripts-3.7/maf_covered_regions.py from 644 to 755 changing mode of build/scripts-3.7/maf_div_sites.py from 644 to 755 changing mode of build/scripts-3.7/maf_drop_overlapping.py from 644 to 755 changing mode of build/scripts-3.7/maf_extract_chrom_ranges.py from 644 to 755 changing mode of build/scripts-3.7/maf_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.7/maf_extract_ranges_indexed.py from 644 to 755 changing mode of build/scripts-3.7/maf_filter.py from 644 to 755 changing mode of build/scripts-3.7/maf_filter_max_wc.py from 644 to 755 changing mode of build/scripts-3.7/maf_gap_frequency.py from 644 to 755 changing mode of build/scripts-3.7/maf_gc_content.py from 644 to 755 changing mode of build/scripts-3.7/maf_interval_alignibility.py from 644 to 755 changing mode of build/scripts-3.7/maf_limit_to_species.py from 644 to 755 changing mode of build/scripts-3.7/maf_mapping_word_frequency.py from 644 to 755 changing mode of build/scripts-3.7/maf_mask_cpg.py from 644 to 755 changing mode of build/scripts-3.7/maf_mean_length_ungapped_piece.py from 644 to 755 changing mode of build/scripts-3.7/maf_percent_columns_matching.py from 644 to 755 changing mode of build/scripts-3.7/maf_percent_identity.py from 644 to 755 changing mode of build/scripts-3.7/maf_print_chroms.py from 644 to 755 changing mode of build/scripts-3.7/maf_print_scores.py from 644 to 755 changing mode of build/scripts-3.7/maf_randomize.py from 644 to 755 changing mode of build/scripts-3.7/maf_region_coverage_by_src.py from 644 to 755 changing mode of build/scripts-3.7/maf_select.py from 644 to 755 changing mode of build/scripts-3.7/maf_shuffle_columns.py from 644 to 755 changing mode of build/scripts-3.7/maf_species_in_all_files.py from 644 to 755 changing mode of build/scripts-3.7/maf_split_by_src.py from 644 to 755 changing mode of build/scripts-3.7/maf_thread_for_species.py from 644 to 755 changing mode of build/scripts-3.7/maf_tile.py from 644 to 755 changing mode of build/scripts-3.7/maf_tile_2.py from 644 to 755 changing mode of build/scripts-3.7/maf_tile_2bit.py from 644 to 755 changing mode of build/scripts-3.7/maf_to_axt.py from 644 to 755 changing mode of build/scripts-3.7/maf_to_concat_fasta.py from 644 to 755 changing mode of build/scripts-3.7/maf_to_fasta.py from 644 to 755 changing mode of build/scripts-3.7/maf_to_int_seqs.py from 644 to 755 changing mode of build/scripts-3.7/maf_translate_chars.py from 644 to 755 changing mode of build/scripts-3.7/maf_truncate.py from 644 to 755 changing mode of build/scripts-3.7/maf_word_frequency.py from 644 to 755 changing mode of build/scripts-3.7/mask_quality.py from 644 to 755 changing mode of build/scripts-3.7/nib_chrom_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.7/nib_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.7/nib_length.py from 644 to 755 changing mode of build/scripts-3.7/one_field_per_line.py from 644 to 755 changing mode of build/scripts-3.7/out_to_chain.py from 644 to 755 changing mode of build/scripts-3.7/prefix_lines.py from 644 to 755 changing mode of build/scripts-3.7/pretty_table.py from 644 to 755 changing mode of build/scripts-3.7/qv_to_bqv.py from 644 to 755 changing mode of build/scripts-3.7/random_lines.py from 644 to 755 changing mode of build/scripts-3.7/table_add_column.py from 644 to 755 changing mode of build/scripts-3.7/table_filter.py from 644 to 755 changing mode of build/scripts-3.7/tfloc_summary.py from 644 to 755 changing mode of build/scripts-3.7/ucsc_gene_table_to_intervals.py from 644 to 755 changing mode of build/scripts-3.7/wiggle_to_array_tree.py from 644 to 755 changing mode of build/scripts-3.7/wiggle_to_binned_array.py from 644 to 755 changing mode of build/scripts-3.7/wiggle_to_chr_binned_array.py from 644 to 755 changing mode of build/scripts-3.7/wiggle_to_simple.py from 644 to 755 SUCCEEDED 00:03:52 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py37-bx-python-0.8.9 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-bx-python-0.8.9 depends on package: py37-six>0 - found ===> py37-bx-python-0.8.9 depends on package: py37-setuptools>0 - found ===> py37-bx-python-0.8.9 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py37-bx-python-0.8.9 ===> py37-bx-python-0.8.9 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-bx-python-0.8.9 depends on package: py37-six>0 - found ===> py37-bx-python-0.8.9 depends on package: py37-setuptools>0 - found ===> py37-bx-python-0.8.9 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list running install running build running build_py running build_ext skipping 'lib/bx/bitset.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date) skipping 'lib/bx/align/_core.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date) skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date) skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date) skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date) skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/array_tree.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bpt_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/cirtree_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bbi_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigwig_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigbed_file.c' Cython extension (up-to-date) skipping 'lib/bx/align/_epo.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/bed.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/wiggle.c' Cython extension (up-to-date) skipping 'lib/bx/align/sitemask/_cpg.c' Cython extension (up-to-date) skipping 'lib/bx/intseq/ngramcount.c' Cython extension (up-to-date) skipping 'lib/bx/misc/_seekbzip2.c' Cython extension (up-to-date) running build_scripts running install_lib creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7 creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages copying build/lib.dragonfly-5.9-x86_64-3.7/psyco_full.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bitset.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/_seqmapping.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/binned_array_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bitset_builders.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bitset_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bitset_utils.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/filter.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/gene_reader.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/interval_index_file.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/interval_index_file_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seqmapping.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seqmapping_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/wiggle.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx copying build/lib.dragonfly-5.9-x86_64-3.7/bx/wiggle_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/_epo.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/_core.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/score_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/score.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/maf_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/axt.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/epo.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/epo_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/lav.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/lav_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/maf.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask/_cpg.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask/cpg.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask/quality.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/sitemask/sitemask_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools/chop.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools/fuse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools/thread.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.9-x86_64-3.7/bx/align/tools/tile.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays copying build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/wiggle.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays copying build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/bed.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays copying build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/array_tree.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays copying build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays copying build/lib.dragonfly-5.9-x86_64-3.7/bx/arrays/array_tree_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bbi_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/cirtree_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bigwig_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bigbed_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bpt_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi copying build/lib.dragonfly-5.9-x86_64-3.7/bx/bbi/bigwig_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook/argparse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook/attribute.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook/doc_optparse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.9-x86_64-3.7/bx/cookbook/progress_bar.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/intersection.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/cluster.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/cluster_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/intersection_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/io.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/random_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/base_coverage.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/complement.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/concat.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/coverage.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/find_clusters.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/intersect.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/join.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/merge.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/quicksect.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intervals/operations/subtract.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intseq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intseq/ngramcount.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intseq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/intseq/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intseq creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/_seekbzip2.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/bgzf.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/bgzf_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/binary_file.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/cdb.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/cdb_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/filecache.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/filecache_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/readlengths.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/seekbzip2.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/seekbzip2_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/seeklzop.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc copying build/lib.dragonfly-5.9-x86_64-3.7/bx/misc/seeklzop_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/_pwm.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/pwm.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/pwm_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/io copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/io/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/io copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/io/transfac.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/io copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/io/transfac_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/io creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/logo copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/logo/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/logo copying build/lib.dragonfly-5.9-x86_64-3.7/bx/motif/logo/template.ps -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/logo creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo copying build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo copying build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo/newick.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo copying build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo/newick_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo copying build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo/phast.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo copying build/lib.dragonfly-5.9-x86_64-3.7/bx/phylo/phast_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/_position_weight_matrix.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/bed_score_aligned_pwm.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/bed_score_aligned_string.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/maf_select_motifs.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/position_weight_matrix.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/pwm_score_maf.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/pwm_score_motifs.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/pwm_score_positions.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm copying build/lib.dragonfly-5.9-x86_64-3.7/bx/pwm/pwm_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/_twobit.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/_nib.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/fasta.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/fasta_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/nib.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/nib_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/qdna.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/qdna_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/seq.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/seq_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/twobit.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq copying build/lib.dragonfly-5.9-x86_64-3.7/bx/seq/twobit_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/tabular copying build/lib.dragonfly-5.9-x86_64-3.7/bx/tabular/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/tabular copying build/lib.dragonfly-5.9-x86_64-3.7/bx/tabular/io.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/tabular creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras copying build/lib.dragonfly-5.9-x86_64-3.7/bx_extras/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras copying build/lib.dragonfly-5.9-x86_64-3.7/bx_extras/fpconst.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras copying build/lib.dragonfly-5.9-x86_64-3.7/bx_extras/fpconst_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras copying build/lib.dragonfly-5.9-x86_64-3.7/bx_extras/lrucache.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras copying build/lib.dragonfly-5.9-x86_64-3.7/bx_extras/pstat.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras copying build/lib.dragonfly-5.9-x86_64-3.7/bx_extras/pyparsing.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras copying build/lib.dragonfly-5.9-x86_64-3.7/bx_extras/stats.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/psyco_full.py to psyco_full.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/binned_array.py to binned_array.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/binned_array_tests.py to binned_array_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bitset_builders.py to bitset_builders.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bitset_tests.py to bitset_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bitset_utils.py to bitset_utils.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/filter.py to filter.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/gene_reader.py to gene_reader.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/interval_index_file.py to interval_index_file.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/interval_index_file_tests.py to interval_index_file_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seqmapping.py to seqmapping.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seqmapping_tests.py to seqmapping_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/wiggle.py to wiggle.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/wiggle_tests.py to wiggle_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/score_tests.py to score_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/score.py to score.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/maf_tests.py to maf_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/axt.py to axt.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/core.py to core.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/epo.py to epo.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/epo_tests.py to epo_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/lav.py to lav.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/lav_tests.py to lav_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/maf.py to maf.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask/core.py to core.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask/cpg.py to cpg.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask/quality.py to quality.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/sitemask/sitemask_tests.py to sitemask_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools/chop.py to chop.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools/fuse.py to fuse.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools/thread.py to thread.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/align/tools/tile.py to tile.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/arrays/array_tree_tests.py to array_tree_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/bbi/bigwig_tests.py to bigwig_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook/argparse.py to argparse.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook/attribute.py to attribute.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook/doc_optparse.py to doc_optparse.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/cookbook/progress_bar.py to progress_bar.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/cluster_tests.py to cluster_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/intersection_tests.py to intersection_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/io.py to io.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/random_intervals.py to random_intervals.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/base_coverage.py to base_coverage.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/complement.py to complement.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/concat.py to concat.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/coverage.py to coverage.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/find_clusters.py to find_clusters.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/intersect.py to intersect.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/join.py to join.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/merge.py to merge.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/quicksect.py to quicksect.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intervals/operations/subtract.py to subtract.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/intseq/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/bgzf_tests.py to bgzf_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/binary_file.py to binary_file.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/cdb.py to cdb.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/cdb_tests.py to cdb_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/filecache.py to filecache.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/filecache_tests.py to filecache_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/readlengths.py to readlengths.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/seekbzip2.py to seekbzip2.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/seekbzip2_tests.py to seekbzip2_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/seeklzop.py to seeklzop.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/misc/seeklzop_tests.py to seeklzop_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/pwm.py to pwm.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/pwm_tests.py to pwm_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/io/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/io/transfac.py to transfac.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/io/transfac_tests.py to transfac_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/motif/logo/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo/newick.py to newick.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo/newick_tests.py to newick_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo/phast.py to phast.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/phylo/phast_tests.py to phast_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/bed_score_aligned_pwm.py to bed_score_aligned_pwm.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/bed_score_aligned_string.py to bed_score_aligned_string.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/maf_select_motifs.py to maf_select_motifs.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/position_weight_matrix.py to position_weight_matrix.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/pwm_score_maf.py to pwm_score_maf.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/pwm_score_motifs.py to pwm_score_motifs.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/pwm_score_positions.py to pwm_score_positions.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/pwm/pwm_tests.py to pwm_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/core.py to core.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/fasta.py to fasta.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/fasta_tests.py to fasta_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/nib.py to nib.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/nib_tests.py to nib_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/qdna.py to qdna.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/qdna_tests.py to qdna_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/seq.py to seq.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/seq_tests.py to seq_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/twobit.py to twobit.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/seq/twobit_tests.py to twobit_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/tabular/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx/tabular/io.py to io.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras/fpconst.py to fpconst.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras/fpconst_tests.py to fpconst_tests.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras/lrucache.py to lrucache.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras/pstat.py to pstat.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras/pyparsing.py to pyparsing.cpython-37.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_extras/stats.py to stats.cpython-37.pyc writing byte-compilation script '/tmp/tmpcwzqaqws.py' /usr/local/bin/python3.7 /tmp/tmpcwzqaqws.py removing /tmp/tmpcwzqaqws.py running install_egg_info running egg_info creating lib/bx_python.egg-info writing lib/bx_python.egg-info/PKG-INFO writing dependency_links to lib/bx_python.egg-info/dependency_links.txt writing requirements to lib/bx_python.egg-info/requires.txt writing top-level names to lib/bx_python.egg-info/top_level.txt writing manifest file 'lib/bx_python.egg-info/SOURCES.txt' reading manifest file 'lib/bx_python.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'distribute_setup.py' writing manifest file 'lib/bx_python.egg-info/SOURCES.txt' Copying lib/bx_python.egg-info to /construction/biology/py-bx-python/stage/usr/local/lib/python3.7/site-packages/bx_python-0.8.9-py3.7.egg-info running install_scripts copying build/scripts-3.7/maf_region_coverage_by_src.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_species_in_all_files.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_filter_max_wc.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/line_select.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/one_field_per_line.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_covered_regions.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_chunk.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/wiggle_to_simple.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/gene_fourfold_sites.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_percent_identity.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_filter.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/nib_intervals_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/get_scores_in_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/interval_join.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/align_print_template.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_print_scores.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_extract_ranges_indexed.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_truncate.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_to_axt.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_count_by_interval.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_diff_basewise_summary.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/nib_length.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/pretty_table.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_merge_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_shuffle_columns.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/table_filter.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_drop_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_to_int_seqs.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/table_add_column.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_build_index.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_gap_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_thread_for_species.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_intersect.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_chop.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_print_chroms.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/div_snp_table_chr.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_complement.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_gc_content.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_tile.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_tile_2.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/axt_to_maf.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/mMK_bitset.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/find_in_sorted_file.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_tile_2bit.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/mask_quality.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/ucsc_gene_table_to_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_mask_cpg.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/wiggle_to_chr_binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/tfloc_summary.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/wiggle_to_binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/lzop_build_offset_table.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_select.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_div_sites.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_build_windows.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/qv_to_bqv.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/aggregate_scores_in_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_interval_alignibility.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/axt_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/axt_to_lav.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_extract_chrom_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_count.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_split_by_src.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_subtract_basewise.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_mapping_word_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_col_counts_all.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_col_counts.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/out_to_chain.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_to_concat_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/axt_extract_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_rand_intersect.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_intersect_basewise.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_extract_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/random_lines.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_coverage.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_count_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_bigwig_profile.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_covered_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_word_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_randomize.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/lav_to_maf.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/interval_count_intersections.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/wiggle_to_array_tree.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_coverage_by_interval.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/int_seqs_to_char_strings.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_limit_to_species.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_mean_length_ungapped_piece.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bed_extend_to.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/bnMapper.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_translate_chars.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/prefix_lines.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/maf_percent_columns_matching.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/nib_chrom_intervals_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.7/lav_to_axt.py -> /construction/biology/py-bx-python/stage/usr/local/bin changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_region_coverage_by_src.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_species_in_all_files.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_filter_max_wc.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/line_select.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/one_field_per_line.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_covered_regions.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_chunk.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_simple.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/gene_fourfold_sites.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_percent_identity.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_filter.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/nib_intervals_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/get_scores_in_intervals.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/interval_join.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/align_print_template.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_print_scores.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_extract_ranges_indexed.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_truncate.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_axt.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_count_by_interval.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_diff_basewise_summary.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/nib_length.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/pretty_table.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_merge_overlapping.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_shuffle_columns.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/table_filter.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_drop_overlapping.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_int_seqs.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/table_add_column.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_build_index.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_gap_frequency.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_thread_for_species.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_intersect.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_chop.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_print_chroms.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/div_snp_table_chr.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_complement.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_gc_content.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_tile.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_tile_2.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_to_maf.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/mMK_bitset.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/find_in_sorted_file.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_tile_2bit.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/mask_quality.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/ucsc_gene_table_to_intervals.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_mask_cpg.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_chr_binned_array.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/tfloc_summary.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_binned_array.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/lzop_build_offset_table.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_select.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_div_sites.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_build_windows.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/qv_to_bqv.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/aggregate_scores_in_intervals.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_interval_alignibility.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_to_lav.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_extract_chrom_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_count.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_split_by_src.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_subtract_basewise.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_mapping_word_frequency.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_col_counts_all.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_col_counts.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/out_to_chain.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_concat_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_extract_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_rand_intersect.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_intersect_basewise.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_extract_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/random_lines.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_coverage.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_count_overlapping.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_bigwig_profile.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_covered_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_word_frequency.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_randomize.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/lav_to_maf.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/interval_count_intersections.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_array_tree.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_coverage_by_interval.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/int_seqs_to_char_strings.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_limit_to_species.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_mean_length_ungapped_piece.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_extend_to.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bnMapper.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_translate_chars.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/prefix_lines.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_percent_columns_matching.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/nib_chrom_intervals_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/lav_to_axt.py to 755 writing list of installed files to '/construction/biology/py-bx-python/.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 00:00:10 ------------------------------------------------------------------------------- -- 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-bx-python-0.8.9 file sizes/checksums [471]: 0% file sizes/checksums [471]: 21% file sizes/checksums [471]: 42% file sizes/checksums [471]: 63% file sizes/checksums [471]: 84% file sizes/checksums [471]: 100% packing files [471]: 0% packing files [471]: 21% packing files [471]: 42% packing files [471]: 63% packing files [471]: 84% packing files [471]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:12 TOTAL TIME 00:05:24