=> Building biology/py-bx-python@py27 Started : Friday, 20 JUL 2018 at 23:28:23 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.242.g757c0-DEVELOPMENT #30: Tue May 8 14:06:27 PDT 2018 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.2-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.2-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/biology/py-bx-python XDG_CONFIG_HOME=/construction/biology/py-bx-python HOME=/construction/biology/py-bx-python TMPDIR="/tmp" PATH=/construction/biology/py-bx-python/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-bx-python XDG_CONFIG_HOME=/construction/biology/py-bx-python HOME=/construction/biology/py-bx-python TMPDIR="/tmp" PATH=/construction/biology/py-bx-python/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/py-bx-python/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/bx-python" EXAMPLESDIR="share/examples/bx-python" DATADIR="share/bx-python" WWWDIR="www/bx-python" ETCDIR="etc/bx-python" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bx-python DOCSDIR=/usr/local/share/doc/bx-python EXAMPLESDIR=/usr/local/share/examples/bx-python WWWDIR=/usr/local/www/bx-python ETCDIR=/usr/local/etc/bx-python -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.2 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500200 OSVERSION=9999999 OSREL=5.2 _OSRELEASE=5.2-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py27-bx-python-0.8.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> py27-bx-python-0.8.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-bx-python-0.8.1_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-bx-python-0.8.1_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-bx-python-0.8.1_1 for building => SHA256 Checksum OK for bxlab-bx-python-0.8.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-bx-python-0.8.1_1 for building ===> Extracting for py27-bx-python-0.8.1_1 => SHA256 Checksum OK for bxlab-bx-python-0.8.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py27-bx-python-0.8.1_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py27-bx-python-0.8.1_1 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.14.3,1.txz Installing py27-numpy-1.14.3,1... `-- Installing gcc5-5.5.0_4... | `-- Installing binutils-2.30_3,1... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | `-- Extracting binutils-2.30_3,1: .......... done | `-- Installing gmp-6.1.2... | `-- Extracting gmp-6.1.2: .......... done | `-- Installing mpc-1.1.0_1... | | `-- Installing mpfr-4.0.1... | | `-- Extracting mpfr-4.0.1: .......... done | `-- Extracting mpc-1.1.0_1: ......... done `-- Extracting gcc5-5.5.0_4: .......... done `-- Installing openblas-0.2.20_2,1... `-- Extracting openblas-0.2.20_2,1: ......... done `-- Installing py27-setuptools-39.2.0... | `-- Installing python27-2.7.15... | | `-- Installing expat-2.2.5... | | `-- Extracting expat-2.2.5: .......... done | | `-- Installing libffi-3.2.1_2... | | `-- Extracting libffi-3.2.1_2: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting python27-2.7.15: .......... done `-- Extracting py27-setuptools-39.2.0: .......... done `-- Installing suitesparse-5.2.0... | `-- Installing lapack-3.5.0_4... | | `-- Installing blas-3.5.0_4... | | `-- Extracting blas-3.5.0_4: ....... done | `-- Extracting lapack-3.5.0_4: .......... done | `-- Installing metis-5.1.0_4... | `-- Extracting metis-5.1.0_4: .......... done `-- Extracting suitesparse-5.2.0: .......... done Extracting py27-numpy-1.14.3,1: .......... done Message from gcc5-5.5.0_4: 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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 6 or newer instead.. Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from metis-5.1.0_4: ===> 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 ===> py27-bx-python-0.8.1_1 depends on package: py27-numpy>0 - found ===> Returning to build of py27-bx-python-0.8.1_1 ===> py27-bx-python-0.8.1_1 depends on package: py27-python-lzo>0 - not found ===> Installing existing package /packages/All/py27-python-lzo-1.12.txz Installing py27-python-lzo-1.12... `-- Installing lzo2-2.10_1... `-- Extracting lzo2-2.10_1: .......... done Extracting py27-python-lzo-1.12: ........ done ===> py27-bx-python-0.8.1_1 depends on package: py27-python-lzo>0 - found ===> Returning to build of py27-bx-python-0.8.1_1 ===> py27-bx-python-0.8.1_1 depends on executable: cython-2.7 - not found ===> Installing existing package /packages/All/py27-cython-0.28.2.txz Installing py27-cython-0.28.2... Extracting py27-cython-0.28.2: .......... done ===> py27-bx-python-0.8.1_1 depends on executable: cython-2.7 - found ===> Returning to build of py27-bx-python-0.8.1_1 ===> py27-bx-python-0.8.1_1 depends on package: py27-setuptools>0 - found ===> py27-bx-python-0.8.1_1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py27-bx-python-0.8.1_1 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py27-bx-python-0.8.1_1 running build running build_py creating build creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7 copying lib/psyco_full.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7 creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/binned_array.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/bitset_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/interval_index_file_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/seqmapping_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/seqmapping.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/bitset_utils.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/filter.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/wiggle.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/binned_array_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/wiggle_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/gene_reader.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/bitset_builders.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx copying lib/bx/interval_index_file.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras copying lib/bx_extras/pyparsing.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras copying lib/bx_extras/fpconst.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras copying lib/bx_extras/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras copying lib/bx_extras/stats.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras copying lib/bx_extras/pstat.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras copying lib/bx_extras/fpconst_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras copying lib/bx_extras/lrucache.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/maf_select_motifs.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/pwm_score_positions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/pwm_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/position_weight_matrix.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm copying lib/bx/pwm/pwm_score_maf.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/twobit.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/nib_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/qdna_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/nib.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/qdna.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/fasta.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/twobit_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/seq.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/fasta_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq copying lib/bx/seq/seq_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/epo.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/score.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/axt.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/epo_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/maf_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/maf.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/lav.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/lav_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align copying lib/bx/align/score_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals copying lib/bx/intervals/io.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals copying lib/bx/intervals/cluster_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals copying lib/bx/intervals/intersection_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals copying lib/bx/intervals/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals copying lib/bx/intervals/random_intervals.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi copying lib/bx/bbi/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi copying lib/bx/bbi/bigwig_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays copying lib/bx/arrays/array_tree_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays copying lib/bx/arrays/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/seeklzop.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/binary_file.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/seekbzip2.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/seekbzip2_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/readlengths.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/cdb.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/seeklzop_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/cdb_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/filecache.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/filecache_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc copying lib/bx/misc/bgzf_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/tabular copying lib/bx/tabular/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/tabular copying lib/bx/tabular/io.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/tabular creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intseq copying lib/bx/intseq/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intseq creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo copying lib/bx/phylo/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo copying lib/bx/phylo/newick_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo copying lib/bx/phylo/phast.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo copying lib/bx/phylo/phast_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo copying lib/bx/phylo/newick.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif copying lib/bx/motif/pwm_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif copying lib/bx/motif/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif copying lib/bx/motif/pwm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook copying lib/bx/cookbook/doc_optparse.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook copying lib/bx/cookbook/argparse.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook copying lib/bx/cookbook/attribute.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook copying lib/bx/cookbook/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook copying lib/bx/cookbook/progress_bar.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools copying lib/bx/align/tools/thread.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools copying lib/bx/align/tools/fuse.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools copying lib/bx/align/tools/tile.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools copying lib/bx/align/tools/chop.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools copying lib/bx/align/tools/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask copying lib/bx/align/sitemask/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask copying lib/bx/align/sitemask/cpg.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask copying lib/bx/align/sitemask/core.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask copying lib/bx/align/sitemask/quality.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/merge.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/base_coverage.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/coverage.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/find_clusters.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/subtract.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/join.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/quicksect.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/intersect.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/complement.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations copying lib/bx/intervals/operations/concat.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/io copying lib/bx/motif/io/transfac_tests.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/io copying lib/bx/motif/io/transfac.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/io copying lib/bx/motif/io/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/io creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/logo copying lib/bx/motif/logo/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/logo copying lib/bx/motif/logo/template.ps -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/logo running build_ext cythoning lib/bx/bitset.pyx to lib/bx/bitset.c building 'bx.bitset' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/kent cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python2.7 -c lib/bx/bitset.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bitset.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python2.7 -c src/binBits.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/binBits.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python2.7 -c src/kent/bits.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/kent/bits.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python2.7 -c src/kent/common.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/kent/common.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bitset.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/binBits.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/kent/bits.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/kent/common.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bitset.so cythoning lib/bx/intervals/intersection.pyx to lib/bx/intervals/intersection.c building 'bx.intervals.intersection' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intervals cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/intervals/intersection.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intervals/intersection.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intervals/intersection.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/intersection.so cythoning lib/bx/align/_core.pyx to lib/bx/align/_core.c building 'bx.align._core' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/align/_core.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/_core.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/_core.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/_core.so cythoning lib/bx/seq/_nib.pyx to lib/bx/seq/_nib.c building 'bx.seq._nib' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/seq cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/seq/_nib.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/seq/_nib.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/seq/_nib.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/_nib.so cythoning lib/bx/seq/_twobit.pyx to lib/bx/seq/_twobit.c building 'bx.seq._twobit' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/seq/_twobit.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/seq/_twobit.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/seq/_twobit.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/_twobit.so cythoning lib/bx/_seqmapping.pyx to lib/bx/_seqmapping.c building 'bx._seqmapping' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/_seqmapping.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/_seqmapping.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/_seqmapping.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/_seqmapping.so cythoning lib/bx/misc/bgzf.pyx to lib/bx/misc/bgzf.c building 'bx.misc.bgzf' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/misc creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/samtools cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/samtools -I/usr/local/include/python2.7 -c lib/bx/misc/bgzf.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/misc/bgzf.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/samtools -I/usr/local/include/python2.7 -c src/samtools/bgzf.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/samtools/bgzf.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/misc/bgzf.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/samtools/bgzf.o -L/usr/local/lib -lz -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/bgzf.so cythoning lib/bx/intervals/cluster.pyx to lib/bx/intervals/cluster.c building 'bx.intervals.cluster' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python2.7 -c lib/bx/intervals/cluster.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intervals/cluster.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python2.7 -c src/cluster.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/cluster.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intervals/cluster.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/cluster.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/cluster.so cythoning lib/bx/pwm/_position_weight_matrix.pyx to lib/bx/pwm/_position_weight_matrix.c building 'bx.pwm._position_weight_matrix' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/pwm cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python2.7 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/pwm/_position_weight_matrix.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python2.7 -c src/pwm_utils.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/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' cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/pwm/_position_weight_matrix.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/pwm_utils.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/_position_weight_matrix.so cythoning lib/bx/motif/_pwm.pyx to lib/bx/motif/_pwm.c building 'bx.motif._pwm' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/motif cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c lib/bx/motif/_pwm.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/motif/_pwm.o In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/motif/_pwm.c:564: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/motif/_pwm.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/_pwm.so cythoning lib/bx/arrays/array_tree.pyx to lib/bx/arrays/array_tree.c building 'bx.arrays.array_tree' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/arrays cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c lib/bx/arrays/array_tree.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/arrays/array_tree.o In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/arrays/array_tree.c:566: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/arrays/array_tree.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/array_tree.so cythoning lib/bx/bbi/bpt_file.pyx to lib/bx/bbi/bpt_file.c building 'bx.bbi.bpt_file' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/bbi/bpt_file.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bpt_file.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bpt_file.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bpt_file.so cythoning lib/bx/bbi/cirtree_file.pyx to lib/bx/bbi/cirtree_file.c building 'bx.bbi.cirtree_file' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/bbi/cirtree_file.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/cirtree_file.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/cirtree_file.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/cirtree_file.so cythoning lib/bx/bbi/bbi_file.pyx to lib/bx/bbi/bbi_file.c building 'bx.bbi.bbi_file' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c lib/bx/bbi/bbi_file.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bbi_file.o In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/bbi/bbi_file.c:566: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bbi_file.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bbi_file.so cythoning lib/bx/bbi/bigwig_file.pyx to lib/bx/bbi/bigwig_file.c building 'bx.bbi.bigwig_file' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c lib/bx/bbi/bigwig_file.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bigwig_file.o In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/bbi/bigwig_file.c:566: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bigwig_file.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bigwig_file.so cythoning lib/bx/bbi/bigbed_file.pyx to lib/bx/bbi/bigbed_file.c building 'bx.bbi.bigbed_file' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c lib/bx/bbi/bigbed_file.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bigbed_file.o In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/bbi/bigbed_file.c:566: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/bbi/bigbed_file.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bigbed_file.so cythoning lib/bx/align/_epo.pyx to lib/bx/align/_epo.c building 'bx.align._epo' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c lib/bx/align/_epo.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/_epo.o In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from lib/bx/align/_epo.c:566: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/_epo.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/_epo.so cythoning lib/bx/arrays/bed.pyx to lib/bx/arrays/bed.c building 'bx.arrays.bed' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/arrays/bed.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/arrays/bed.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/arrays/bed.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/bed.so cythoning lib/bx/arrays/wiggle.pyx to lib/bx/arrays/wiggle.c warning: lib/bx/arrays/wiggle.pyx:94:20: Unreachable code building 'bx.arrays.wiggle' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/arrays/wiggle.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/arrays/wiggle.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/arrays/wiggle.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/wiggle.so cythoning lib/bx/align/sitemask/_cpg.pyx to lib/bx/align/sitemask/_cpg.c building 'bx.align.sitemask._cpg' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/sitemask cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/align/sitemask/_cpg.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/sitemask/_cpg.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c lib/bx/align/sitemask/find_cpg.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/sitemask/find_cpg.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/sitemask/_cpg.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/align/sitemask/find_cpg.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask/_cpg.so cythoning lib/bx/intseq/ngramcount.pyx to lib/bx/intseq/ngramcount.c building 'bx.intseq.ngramcount' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intseq cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python2.7 -c lib/bx/intseq/ngramcount.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intseq/ngramcount.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/intseq/ngramcount.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intseq/ngramcount.so cythoning lib/bx/misc/_seekbzip2.pyx to lib/bx/misc/_seekbzip2.c building 'bx.misc._seekbzip2' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/bunzip cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/bunzip -I/usr/local/include/python2.7 -c lib/bx/misc/_seekbzip2.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/misc/_seekbzip2.o cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/bunzip -I/usr/local/include/python2.7 -c src/bunzip/micro-bunzip.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/bunzip/micro-bunzip.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/lib/bx/misc/_seekbzip2.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/src/bunzip/micro-bunzip.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/_seekbzip2.so running build_scripts creating build/scripts-2.7 copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-2.7 copying and adjusting scripts/maf_translate_chars.py -> build/scripts-2.7 copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-2.7 copying and adjusting scripts/maf_chop.py -> build/scripts-2.7 copying and adjusting scripts/maf_tile.py -> build/scripts-2.7 copying and adjusting scripts/maf_split_by_src.py -> build/scripts-2.7 copying and adjusting scripts/bnMapper.py -> build/scripts-2.7 copying and adjusting scripts/maf_build_index.py -> build/scripts-2.7 copying and adjusting scripts/pretty_table.py -> build/scripts-2.7 copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-2.7 copying and adjusting scripts/bed_intersect.py -> build/scripts-2.7 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-2.7 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-2.7 copying and adjusting scripts/out_to_chain.py -> build/scripts-2.7 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-2.7 copying and adjusting scripts/table_filter.py -> build/scripts-2.7 copying and adjusting scripts/maf_col_counts.py -> build/scripts-2.7 copying and adjusting scripts/maf_div_sites.py -> build/scripts-2.7 copying and adjusting scripts/mMK_bitset.py -> build/scripts-2.7 copying and adjusting scripts/random_lines.py -> build/scripts-2.7 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-2.7 copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-2.7 copying and adjusting scripts/table_add_column.py -> build/scripts-2.7 copying and adjusting scripts/maf_chunk.py -> build/scripts-2.7 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-2.7 copying and adjusting scripts/maf_covered_regions.py -> build/scripts-2.7 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-2.7 copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-2.7 copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-2.7 copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-2.7 copying and adjusting scripts/maf_filter.py -> build/scripts-2.7 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-2.7 copying and adjusting scripts/bed_coverage.py -> build/scripts-2.7 copying and adjusting scripts/maf_gc_content.py -> build/scripts-2.7 copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-2.7 copying and adjusting scripts/maf_select.py -> build/scripts-2.7 copying and adjusting scripts/maf_truncate.py -> build/scripts-2.7 copying and adjusting scripts/bed_complement.py -> build/scripts-2.7 copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-2.7 copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-2.7 copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-2.7 copying and adjusting scripts/lav_to_maf.py -> build/scripts-2.7 copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-2.7 copying and adjusting scripts/nib_length.py -> build/scripts-2.7 copying and adjusting scripts/align_print_template.py -> build/scripts-2.7 copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-2.7 copying and adjusting scripts/bed_build_windows.py -> build/scripts-2.7 copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-2.7 copying and adjusting scripts/line_select.py -> build/scripts-2.7 copying and adjusting scripts/maf_count.py -> build/scripts-2.7 copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-2.7 copying and adjusting scripts/maf_to_fasta.py -> build/scripts-2.7 copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-2.7 copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-2.7 copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-2.7 copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-2.7 copying and adjusting scripts/axt_to_lav.py -> build/scripts-2.7 copying and adjusting scripts/maf_randomize.py -> build/scripts-2.7 copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-2.7 copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-2.7 copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-2.7 copying and adjusting scripts/maf_tile_2.py -> build/scripts-2.7 copying and adjusting scripts/tfloc_summary.py -> build/scripts-2.7 copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-2.7 copying and adjusting scripts/lav_to_axt.py -> build/scripts-2.7 copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-2.7 copying and adjusting scripts/interval_count_intersections.py -> build/scripts-2.7 copying and adjusting scripts/maf_percent_identity.py -> build/scripts-2.7 copying and adjusting scripts/maf_word_frequency.py -> build/scripts-2.7 copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-2.7 copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-2.7 copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-2.7 copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-2.7 copying and adjusting scripts/axt_to_maf.py -> build/scripts-2.7 copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-2.7 copying and adjusting scripts/qv_to_bqv.py -> build/scripts-2.7 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-2.7 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-2.7 copying and adjusting scripts/mask_quality.py -> build/scripts-2.7 copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-2.7 copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-2.7 copying and adjusting scripts/axt_to_fasta.py -> build/scripts-2.7 copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-2.7 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-2.7 copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-2.7 copying and adjusting scripts/interval_join.py -> build/scripts-2.7 copying and adjusting scripts/prefix_lines.py -> build/scripts-2.7 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-2.7 copying and adjusting scripts/bed_extend_to.py -> build/scripts-2.7 copying and adjusting scripts/one_field_per_line.py -> build/scripts-2.7 copying and adjusting scripts/maf_print_scores.py -> build/scripts-2.7 copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-2.7 copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-2.7 copying and adjusting scripts/maf_to_axt.py -> build/scripts-2.7 changing mode of build/scripts-2.7/bed_bigwig_profile.py from 644 to 755 changing mode of build/scripts-2.7/maf_translate_chars.py from 644 to 755 changing mode of build/scripts-2.7/maf_col_counts_all.py from 644 to 755 changing mode of build/scripts-2.7/maf_chop.py from 644 to 755 changing mode of build/scripts-2.7/maf_tile.py from 644 to 755 changing mode of build/scripts-2.7/maf_split_by_src.py from 644 to 755 changing mode of build/scripts-2.7/bnMapper.py from 644 to 755 changing mode of build/scripts-2.7/maf_build_index.py from 644 to 755 changing mode of build/scripts-2.7/pretty_table.py from 644 to 755 changing mode of build/scripts-2.7/int_seqs_to_char_strings.py from 644 to 755 changing mode of build/scripts-2.7/bed_intersect.py from 644 to 755 changing mode of build/scripts-2.7/bed_count_by_interval.py from 644 to 755 changing mode of build/scripts-2.7/maf_print_chroms.py from 644 to 755 changing mode of build/scripts-2.7/out_to_chain.py from 644 to 755 changing mode of build/scripts-2.7/axt_extract_ranges.py from 644 to 755 changing mode of build/scripts-2.7/table_filter.py from 644 to 755 changing mode of build/scripts-2.7/maf_col_counts.py from 644 to 755 changing mode of build/scripts-2.7/maf_div_sites.py from 644 to 755 changing mode of build/scripts-2.7/mMK_bitset.py from 644 to 755 changing mode of build/scripts-2.7/random_lines.py from 644 to 755 changing mode of build/scripts-2.7/wiggle_to_array_tree.py from 644 to 755 changing mode of build/scripts-2.7/bed_subtract_basewise.py from 644 to 755 changing mode of build/scripts-2.7/table_add_column.py from 644 to 755 changing mode of build/scripts-2.7/maf_chunk.py from 644 to 755 changing mode of build/scripts-2.7/maf_mean_length_ungapped_piece.py from 644 to 755 changing mode of build/scripts-2.7/maf_covered_regions.py from 644 to 755 changing mode of build/scripts-2.7/bed_intersect_basewise.py from 644 to 755 changing mode of build/scripts-2.7/maf_extract_chrom_ranges.py from 644 to 755 changing mode of build/scripts-2.7/bed_diff_basewise_summary.py from 644 to 755 changing mode of build/scripts-2.7/ucsc_gene_table_to_intervals.py from 644 to 755 changing mode of build/scripts-2.7/maf_filter.py from 644 to 755 changing mode of build/scripts-2.7/maf_percent_columns_matching.py from 644 to 755 changing mode of build/scripts-2.7/bed_coverage.py from 644 to 755 changing mode of build/scripts-2.7/maf_gc_content.py from 644 to 755 changing mode of build/scripts-2.7/wiggle_to_binned_array.py from 644 to 755 changing mode of build/scripts-2.7/maf_select.py from 644 to 755 changing mode of build/scripts-2.7/maf_truncate.py from 644 to 755 changing mode of build/scripts-2.7/bed_complement.py from 644 to 755 changing mode of build/scripts-2.7/maf_covered_ranges.py from 644 to 755 changing mode of build/scripts-2.7/find_in_sorted_file.py from 644 to 755 changing mode of build/scripts-2.7/maf_interval_alignibility.py from 644 to 755 changing mode of build/scripts-2.7/lav_to_maf.py from 644 to 755 changing mode of build/scripts-2.7/bed_coverage_by_interval.py from 644 to 755 changing mode of build/scripts-2.7/nib_length.py from 644 to 755 changing mode of build/scripts-2.7/align_print_template.py from 644 to 755 changing mode of build/scripts-2.7/maf_gap_frequency.py from 644 to 755 changing mode of build/scripts-2.7/bed_build_windows.py from 644 to 755 changing mode of build/scripts-2.7/aggregate_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-2.7/line_select.py from 644 to 755 changing mode of build/scripts-2.7/maf_count.py from 644 to 755 changing mode of build/scripts-2.7/maf_region_coverage_by_src.py from 644 to 755 changing mode of build/scripts-2.7/maf_to_fasta.py from 644 to 755 changing mode of build/scripts-2.7/maf_to_concat_fasta.py from 644 to 755 changing mode of build/scripts-2.7/maf_to_int_seqs.py from 644 to 755 changing mode of build/scripts-2.7/maf_mapping_word_frequency.py from 644 to 755 changing mode of build/scripts-2.7/maf_drop_overlapping.py from 644 to 755 changing mode of build/scripts-2.7/axt_to_lav.py from 644 to 755 changing mode of build/scripts-2.7/maf_randomize.py from 644 to 755 changing mode of build/scripts-2.7/maf_limit_to_species.py from 644 to 755 changing mode of build/scripts-2.7/get_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-2.7/lzop_build_offset_table.py from 644 to 755 changing mode of build/scripts-2.7/maf_tile_2.py from 644 to 755 changing mode of build/scripts-2.7/tfloc_summary.py from 644 to 755 changing mode of build/scripts-2.7/maf_extract_ranges.py from 644 to 755 changing mode of build/scripts-2.7/lav_to_axt.py from 644 to 755 changing mode of build/scripts-2.7/bed_count_overlapping.py from 644 to 755 changing mode of build/scripts-2.7/interval_count_intersections.py from 644 to 755 changing mode of build/scripts-2.7/maf_percent_identity.py from 644 to 755 changing mode of build/scripts-2.7/maf_word_frequency.py from 644 to 755 changing mode of build/scripts-2.7/div_snp_table_chr.py from 644 to 755 changing mode of build/scripts-2.7/maf_tile_2bit.py from 644 to 755 changing mode of build/scripts-2.7/maf_thread_for_species.py from 644 to 755 changing mode of build/scripts-2.7/maf_extract_ranges_indexed.py from 644 to 755 changing mode of build/scripts-2.7/axt_to_maf.py from 644 to 755 changing mode of build/scripts-2.7/maf_mask_cpg.py from 644 to 755 changing mode of build/scripts-2.7/qv_to_bqv.py from 644 to 755 changing mode of build/scripts-2.7/nib_chrom_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-2.7/bed_merge_overlapping.py from 644 to 755 changing mode of build/scripts-2.7/mask_quality.py from 644 to 755 changing mode of build/scripts-2.7/wiggle_to_chr_binned_array.py from 644 to 755 changing mode of build/scripts-2.7/gene_fourfold_sites.py from 644 to 755 changing mode of build/scripts-2.7/axt_to_fasta.py from 644 to 755 changing mode of build/scripts-2.7/nib_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-2.7/wiggle_to_simple.py from 644 to 755 changing mode of build/scripts-2.7/maf_species_in_all_files.py from 644 to 755 changing mode of build/scripts-2.7/interval_join.py from 644 to 755 changing mode of build/scripts-2.7/prefix_lines.py from 644 to 755 changing mode of build/scripts-2.7/maf_shuffle_columns.py from 644 to 755 changing mode of build/scripts-2.7/bed_extend_to.py from 644 to 755 changing mode of build/scripts-2.7/one_field_per_line.py from 644 to 755 changing mode of build/scripts-2.7/maf_print_scores.py from 644 to 755 changing mode of build/scripts-2.7/bed_rand_intersect.py from 644 to 755 changing mode of build/scripts-2.7/maf_filter_max_wc.py from 644 to 755 changing mode of build/scripts-2.7/maf_to_axt.py from 644 to 755 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py27-bx-python-0.8.1_1 depends on package: py27-numpy>0 - found ===> py27-bx-python-0.8.1_1 depends on package: py27-python-lzo>0 - found ===> py27-bx-python-0.8.1_1 depends on package: py27-setuptools>0 - found ===> py27-bx-python-0.8.1_1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py27-bx-python-0.8.1_1 ===> 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/python2.7 creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras/fpconst.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras/fpconst_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras/stats.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras/pyparsing.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras/lrucache.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx_extras/pstat.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/psyco_full.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/_seqmapping.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/_position_weight_matrix.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/position_weight_matrix.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/pwm_score_positions.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/pwm_score_maf.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/maf_select_motifs.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/bed_score_aligned_pwm.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/bed_score_aligned_string.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/pwm_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/pwm/pwm_score_motifs.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seqmapping_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bitset.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/filter.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/fasta_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/twobit_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/seq.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/twobit.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/nib.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/fasta.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/qdna.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/qdna_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/seq_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/nib_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/_twobit.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seq/_nib.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bitset_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/wiggle_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/intersection.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/io.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/random_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/cluster_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/intersection_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/base_coverage.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/quicksect.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/subtract.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/merge.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/concat.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/join.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/intersect.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/find_clusters.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/coverage.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/complement.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/operations/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intervals/cluster.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/interval_index_file_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bitset_utils.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/_core.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools/fuse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools/tile.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools/chop.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/tools/thread.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/maf_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/score.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask/_cpg.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask/cpg.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask/quality.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/sitemask/sitemask_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/axt.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/epo_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/score_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/lav_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/lav.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/epo.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/maf.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/align/_epo.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bigwig_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bigwig_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/cirtree_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bpt_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bigbed_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bbi/bbi_file.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/array_tree_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/bed.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/wiggle.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/arrays/array_tree.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/interval_index_file.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/seekbzip2.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/seeklzop.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/filecache_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/binary_file.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/readlengths.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/cdb_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/seeklzop_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/seekbzip2_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/cdb.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/filecache.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/bgzf_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/bgzf.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/misc/_seekbzip2.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/pwm.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/logo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/logo/template.ps -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/logo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/logo/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/logo creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/io copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/io/transfac_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/io copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/io/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/io copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/io/transfac.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/io copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/pwm_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/motif/_pwm.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/tabular copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/tabular/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/tabular copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/tabular/io.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/tabular copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/wiggle.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo/phast_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo/phast.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo/newick_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/phylo/newick.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/seqmapping.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/bitset_builders.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/gene_reader.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/binned_array_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook/attribute.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook/progress_bar.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook/doc_optparse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook/argparse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/cookbook/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook creating /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intseq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intseq/ngramcount.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intseq copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/bx/intseq/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intseq byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras/fpconst.py to fpconst.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras/fpconst_tests.py to fpconst_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras/stats.py to stats.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras/pyparsing.py to pyparsing.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras/lrucache.py to lrucache.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx_extras/pstat.py to pstat.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/psyco_full.py to psyco_full.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/position_weight_matrix.py to position_weight_matrix.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/pwm_score_positions.py to pwm_score_positions.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/pwm_score_maf.py to pwm_score_maf.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/maf_select_motifs.py to maf_select_motifs.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/bed_score_aligned_pwm.py to bed_score_aligned_pwm.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/bed_score_aligned_string.py to bed_score_aligned_string.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/pwm_tests.py to pwm_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/pwm/pwm_score_motifs.py to pwm_score_motifs.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seqmapping_tests.py to seqmapping_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/filter.py to filter.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/fasta_tests.py to fasta_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/twobit_tests.py to twobit_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/seq.py to seq.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/twobit.py to twobit.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/nib.py to nib.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/fasta.py to fasta.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/qdna.py to qdna.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/qdna_tests.py to qdna_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/seq_tests.py to seq_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/core.py to core.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seq/nib_tests.py to nib_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bitset_tests.py to bitset_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/wiggle_tests.py to wiggle_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/io.py to io.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/random_intervals.py to random_intervals.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/cluster_tests.py to cluster_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/intersection_tests.py to intersection_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/base_coverage.py to base_coverage.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/quicksect.py to quicksect.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/subtract.py to subtract.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/merge.py to merge.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/concat.py to concat.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/join.py to join.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/intersect.py to intersect.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/find_clusters.py to find_clusters.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/coverage.py to coverage.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/complement.py to complement.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intervals/operations/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/interval_index_file_tests.py to interval_index_file_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bitset_utils.py to bitset_utils.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools/fuse.py to fuse.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools/tile.py to tile.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools/chop.py to chop.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/tools/thread.py to thread.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/maf_tests.py to maf_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/core.py to core.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/score.py to score.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask/cpg.py to cpg.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask/quality.py to quality.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask/core.py to core.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/sitemask/sitemask_tests.py to sitemask_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/axt.py to axt.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/epo_tests.py to epo_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/score_tests.py to score_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/lav_tests.py to lav_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/lav.py to lav.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/epo.py to epo.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/align/maf.py to maf.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi/bigwig_tests.py to bigwig_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bbi/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays/array_tree_tests.py to array_tree_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/arrays/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/interval_index_file.py to interval_index_file.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/seekbzip2.py to seekbzip2.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/seeklzop.py to seeklzop.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/filecache_tests.py to filecache_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/binary_file.py to binary_file.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/readlengths.py to readlengths.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/cdb_tests.py to cdb_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/seeklzop_tests.py to seeklzop_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/seekbzip2_tests.py to seekbzip2_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/cdb.py to cdb.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/filecache.py to filecache.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/misc/bgzf_tests.py to bgzf_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/pwm.py to pwm.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/logo/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/io/transfac_tests.py to transfac_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/io/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/io/transfac.py to transfac.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/motif/pwm_tests.py to pwm_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/tabular/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/tabular/io.py to io.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/wiggle.py to wiggle.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo/phast_tests.py to phast_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo/phast.py to phast.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo/newick_tests.py to newick_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/phylo/newick.py to newick.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/binned_array.py to binned_array.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/seqmapping.py to seqmapping.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/bitset_builders.py to bitset_builders.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/gene_reader.py to gene_reader.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/binned_array_tests.py to binned_array_tests.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook/attribute.py to attribute.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook/progress_bar.py to progress_bar.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook/doc_optparse.py to doc_optparse.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook/argparse.py to argparse.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/cookbook/__init__.py to __init__.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python2.7/site-packages/bx/intseq/__init__.py to __init__.pyc writing byte-compilation script '/tmp/tmpNJRFsk.py' /usr/local/bin/python2.7 -O /tmp/tmpNJRFsk.py removing /tmp/tmpNJRFsk.py running install_egg_info running egg_info creating lib/bx_python.egg-info writing requirements to lib/bx_python.egg-info/requires.txt writing lib/bx_python.egg-info/PKG-INFO writing top-level names to lib/bx_python.egg-info/top_level.txt writing dependency_links to lib/bx_python.egg-info/dependency_links.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/python2.7/site-packages/bx_python-0.8.1-py2.7.egg-info running install_scripts copying build/scripts-2.7/int_seqs_to_char_strings.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_extract_chrom_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_tile.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_print_chroms.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_chop.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_diff_basewise_summary.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/out_to_chain.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_subtract_basewise.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_bigwig_profile.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_div_sites.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_build_index.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/pretty_table.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_translate_chars.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/axt_extract_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/wiggle_to_array_tree.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/table_add_column.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_intersect_basewise.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/table_filter.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/mMK_bitset.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_col_counts_all.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_intersect.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_split_by_src.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_mean_length_ungapped_piece.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_chunk.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_covered_regions.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_col_counts.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/random_lines.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_count_by_interval.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bnMapper.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/one_field_per_line.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_coverage_by_interval.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_build_windows.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/lav_to_maf.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/lzop_build_offset_table.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/gene_fourfold_sites.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_count.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_percent_identity.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/nib_length.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/axt_to_maf.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_merge_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/axt_to_lav.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_percent_columns_matching.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/axt_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_gc_content.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/line_select.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/nib_chrom_intervals_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_extract_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/ucsc_gene_table_to_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_extend_to.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_filter.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_species_in_all_files.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/tfloc_summary.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_truncate.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_complement.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_covered_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_coverage.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/prefix_lines.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_tile_2bit.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/qv_to_bqv.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_randomize.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/wiggle_to_chr_binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/nib_intervals_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_limit_to_species.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_filter_max_wc.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_region_coverage_by_src.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_select.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_mask_cpg.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_to_int_seqs.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_to_axt.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_to_concat_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_count_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/lav_to_axt.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_interval_alignibility.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_thread_for_species.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_gap_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/aggregate_scores_in_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_extract_ranges_indexed.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/wiggle_to_simple.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_print_scores.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/align_print_template.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_mapping_word_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_shuffle_columns.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/get_scores_in_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_drop_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/interval_count_intersections.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/wiggle_to_binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/div_snp_table_chr.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/interval_join.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/mask_quality.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_tile_2.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/bed_rand_intersect.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/maf_word_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-2.7/find_in_sorted_file.py -> /construction/biology/py-bx-python/stage/usr/local/bin 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_extract_chrom_ranges.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_print_chroms.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/bed_diff_basewise_summary.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/bed_subtract_basewise.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_div_sites.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/pretty_table.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/axt_extract_ranges.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/table_add_column.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/table_filter.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/maf_col_counts_all.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_split_by_src.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/maf_chunk.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_col_counts.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_count_by_interval.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/one_field_per_line.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/bed_build_windows.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/lzop_build_offset_table.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_count.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/nib_length.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/bed_merge_overlapping.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_percent_columns_matching.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/maf_gc_content.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/nib_chrom_intervals_to_fasta.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/ucsc_gene_table_to_intervals.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/maf_filter.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/tfloc_summary.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/bed_complement.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/bed_coverage.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/prefix_lines.py to 755 changing mode of 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/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/maf_to_axt.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/bed_count_overlapping.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/lav_to_axt.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/maf_interval_alignibility.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/maf_gap_frequency.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_extract_ranges_indexed.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/maf_print_scores.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_mapping_word_frequency.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/get_scores_in_intervals.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/interval_count_intersections.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/div_snp_table_chr.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/mask_quality.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/bed_rand_intersect.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/find_in_sorted_file.py to 755 writing list of installed files to '/construction/biology/py-bx-python/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py27-bx-python-0.8.1_1 file sizes/checksums [474]: ..... done packing files [474]: ..... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 20 JUL 2018 at 23:30:55 UTC Duration: 00:02:31