=> Building biology/pycogent@py27 Started : Friday, 20 JUL 2018 at 23:30:58 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/pycogent XDG_CONFIG_HOME=/construction/biology/pycogent HOME=/construction/biology/pycogent TMPDIR="/tmp" PATH=/construction/biology/pycogent/.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/pycogent XDG_CONFIG_HOME=/construction/biology/pycogent HOME=/construction/biology/pycogent TMPDIR="/tmp" PATH=/construction/biology/pycogent/.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/pycogent/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/pycogent" EXAMPLESDIR="share/examples/pycogent" DATADIR="share/pycogent" WWWDIR="www/pycogent" ETCDIR="etc/pycogent" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pycogent DOCSDIR=/usr/local/share/doc/pycogent EXAMPLESDIR=/usr/local/share/examples/pycogent WWWDIR=/usr/local/www/pycogent ETCDIR=/usr/local/etc/pycogent -------------------------------------------------- -- /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 GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> pycogent-1.9_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 ===> pycogent-1.9_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pycogent-1.9_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by pycogent-1.9_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by pycogent-1.9_1 for building => SHA256 Checksum OK for pycogent-pycogent-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by pycogent-1.9_1 for building ===> Extracting for pycogent-1.9_1 => SHA256 Checksum OK for pycogent-pycogent-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for pycogent-1.9_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> pycogent-1.9_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 ===> pycogent-1.9_1 depends on package: py27-numpy>0 - found ===> Returning to build of pycogent-1.9_1 ===> pycogent-1.9_1 depends on package: py27-sphinx>=0 - not found ===> Installing existing package /packages/All/py27-sphinx-1.6.5_1,1.txz Installing py27-sphinx-1.6.5_1,1... `-- Installing ca_root_nss-3.38... `-- Extracting ca_root_nss-3.38: ........ done `-- Installing py27-Babel-2.5.3... | `-- Installing py27-pytz-2018.5,1... | `-- Extracting py27-pytz-2018.5,1: .......... done `-- Extracting py27-Babel-2.5.3: .......... done `-- Installing py27-Jinja2-2.10... | `-- Installing py27-MarkupSafe-1.0... | `-- Extracting py27-MarkupSafe-1.0: .......... done `-- Extracting py27-Jinja2-2.10: .......... done `-- Installing py27-alabaster-0.7.6... `-- Extracting py27-alabaster-0.7.6: .......... done `-- Installing py27-docutils-0.14_3... `-- Extracting py27-docutils-0.14_3: .......... done `-- Installing py27-imagesize-0.7.1... `-- Extracting py27-imagesize-0.7.1: .......... done `-- Installing py27-pygments-2.2.0... `-- Extracting py27-pygments-2.2.0: .......... done `-- Installing py27-requests-2.18.4... | `-- Installing py27-certifi-2018.4.16... | `-- Extracting py27-certifi-2018.4.16: .......... done | `-- Installing py27-chardet-3.0.4... | `-- Extracting py27-chardet-3.0.4: .......... done | `-- Installing py27-idna-2.6... | `-- Extracting py27-idna-2.6: .......... done | `-- Installing py27-urllib3-1.22,1... | | `-- Installing py27-cryptography-2.1.4... | | `-- Installing py27-asn1crypto-0.22.0... | | `-- Extracting py27-asn1crypto-0.22.0: .......... done | | `-- Installing py27-cffi-1.11.5... | | | `-- Installing py27-pycparser-2.18... | | | `-- Extracting py27-pycparser-2.18: .......... done | | `-- Extracting py27-cffi-1.11.5: .......... done | | `-- Installing py27-enum34-1.1.6... | | `-- Extracting py27-enum34-1.1.6: .......... done | | `-- Installing py27-ipaddress-1.0.22... | | `-- Extracting py27-ipaddress-1.0.22: .......... done | | `-- Installing py27-six-1.11.0... | | `-- Extracting py27-six-1.11.0: .......... done | | `-- Extracting py27-cryptography-2.1.4: .......... done | | `-- Installing py27-openssl-17.5.0_1... | | `-- Extracting py27-openssl-17.5.0_1: .......... done | | `-- Installing py27-pysocks-1.6.8... | | `-- Extracting py27-pysocks-1.6.8: .......... done | `-- Extracting py27-urllib3-1.22,1: .......... done `-- Extracting py27-requests-2.18.4: .......... done `-- Installing py27-snowballstemmer-1.2.0_1... | `-- Installing py27-pystemmer-1.3.0_1... | `-- Extracting py27-pystemmer-1.3.0_1: ......... done `-- Extracting py27-snowballstemmer-1.2.0_1: .......... done `-- Installing py27-sphinx_rtd_theme-0.4.0... `-- Extracting py27-sphinx_rtd_theme-0.4.0: .......... done `-- Installing py27-sphinxcontrib-websupport-1.0.1... `-- Extracting py27-sphinxcontrib-websupport-1.0.1: .......... done `-- Installing py27-typing-3.6.4... `-- Extracting py27-typing-3.6.4: .......... done Extracting py27-sphinx-1.6.5_1,1: .......... done Message from ca_root_nss-3.38: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** Message from py27-urllib3-1.22,1: Be careful, support of IPv6 is broken with PySocks 1.5.7. ===> pycogent-1.9_1 depends on package: py27-sphinx>=0 - found ===> Returning to build of pycogent-1.9_1 ===> pycogent-1.9_1 depends on package: py27-sqlalchemy10>=1.0.13 - not found ===> Installing existing package /packages/All/py27-sqlalchemy10-1.0.14.txz Installing py27-sqlalchemy10-1.0.14... `-- Installing py27-sqlite3-2.7.15_7... | `-- Installing sqlite3-3.24.0_1... | `-- Extracting sqlite3-3.24.0_1: .......... done `-- Extracting py27-sqlite3-2.7.15_7: ........ done Extracting py27-sqlalchemy10-1.0.14: .......... done ===> pycogent-1.9_1 depends on package: py27-sqlalchemy10>=1.0.13 - found ===> Returning to build of pycogent-1.9_1 ===> pycogent-1.9_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 ===> pycogent-1.9_1 depends on executable: cython-2.7 - found ===> Returning to build of pycogent-1.9_1 ===> pycogent-1.9_1 depends on package: py27-setuptools>0 - found ===> pycogent-1.9_1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for pycogent-1.9_1 warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pyx:14:0: 'stdlib' is deprecated, use 'libc.stdlib' warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/struct/_asa.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/struct/_contact.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' Compiling cogent/evolve/_pairwise_distance.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/struct/_asa.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/struct/_contact.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/maths/_period.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/maths/spatial/ckd3.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. [1/5] Cythonizing cogent/evolve/_pairwise_distance.pyx [2/5] Cythonizing cogent/maths/_period.pyx [3/5] Cythonizing cogent/maths/spatial/ckd3.pyx [4/5] Cythonizing cogent/struct/_asa.pyx [5/5] Cythonizing cogent/struct/_contact.pyx running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for pycogent-1.9_1 running build running build_py creating build creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7 creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent copying cogent/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/align.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/indel_model.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/progressive.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/traceback.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/indel_positions.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/dp_calculation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/pycompare.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/algorithm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align copying cogent/align/pairwise.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/weights copying cogent/align/weights/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/weights copying cogent/align/weights/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/weights copying cogent/align/weights/methods.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/weights creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/mothur.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/msms.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnaview.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rdp_classifier.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rdp_classifier20.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/nupack.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnaforester.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/sfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/mfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/sfffile.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnashapes.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rtax.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/raxml_v730.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/parsinsert.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pandaseq.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/unafold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/raxml.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/stride.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pplacer.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/mafft.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/parameters.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/seqprep.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnaalifold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/muscle.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/muscle_v38.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/sffinfo.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pknotsrg.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/uclust.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/vienna_package.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/usearch.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cdbfasta.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cove.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cmfinder.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/gctmpca.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/flash.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/infernal.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/formatdb.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/fasttree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/blast.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cd_hit.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/ilm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/contrafold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/bwa.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/consan.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/dotur.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/fasttree_v1.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/guppy.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/dialign.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/knetfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/carnac.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/foldalign.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/comrna.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/fastq_join.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/blat.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/clustalw.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/clearcut.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app copying cogent/app/dynalign.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/procrustes.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/metric_scaling.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/UPGMA.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/goodness_of_fit.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/approximate_mds.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/nmds.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/genetic_code.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/location.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/sequence.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/annotation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/tree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/info.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/alphabet.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/moltype.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/usage.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/entity.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/bitvector.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/alignment.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core copying cogent/core/profile.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data copying cogent/data/molecular_weight.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data copying cogent/data/protein_properties.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data copying cogent/data/nucleic_properties.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data copying cogent/data/ligand_properties.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data copying cogent/data/energy_params.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data copying cogent/data/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db copying cogent/db/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db copying cogent/db/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db copying cogent/db/rfam.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db copying cogent/db/ncbi.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db copying cogent/db/pdb.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/region.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/name.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/host.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/sequence.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/related_region.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/compara.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/feature_level.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/database.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/assembly.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/genome.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/species.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/dinuc.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/arrow_rates.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/dendrogram.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/compatibility.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/linear.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/distribution_plots.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/rlg2mpl.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/dotplot.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/codon_usage.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/legend.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/multivariate_plot.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/fancy_arrow.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/discrete_markov.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/coevolution.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_calculation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/substitution_calculation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_function.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/parameter_controller.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/predicate.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/simulate.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/solved_models.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/best_likelihood.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_tree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/pairwise_distance.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/substitution_model.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/bootstrap.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/motif_prob_model.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/models.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/phylip.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/nexus.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/structure.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/pdb_color.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/xyzrn.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/mage.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/fasta.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/rna_struct.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/table.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/motif.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/alignment.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/clustal.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/pdb.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/stockholm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/bedgraph.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format copying cogent/format/text_tree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/scipy_optimize.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/geometry.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/optimisers.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/period.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/distance_transform.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/matrix_exponentiation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/markov.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/solve.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/scipy_optimisers.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/simannealingoptimiser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/function_optimisation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/fit_function.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/matrix_exponential_integration.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/svd.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/matrix_logarithm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix copying cogent/maths/matrix/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix copying cogent/maths/matrix/distance.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/information_criteria.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/special.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/histogram.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/ks.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/kendall.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/rarefaction.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/distribution.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/jackknife.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/period.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/test.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/alpha_diversity.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/get_by_cai.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/adaptor.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_tree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_unifrac.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/unifrac creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/spatial copying cogent/maths/spatial/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/spatial creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/motif copying cogent/motif/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/motif copying cogent/motif/k_word.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/motif copying cogent/motif/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/motif creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/bpseq.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/hmmscan.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/msms.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/illumina_sequence.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnaview.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/tree_xml.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/binary_sff.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rna_plot.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ncbi_taxonomy.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ilm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/macsim.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_ko.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnashapes.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/locuslink.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnaalifold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rfam.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/clustal.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/tree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gbseq.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/greengenes.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/flowgram_parser.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/dotur.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/contrafold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/agilent_microarray.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/structure.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gcg.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/flowgram.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cove.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/dialign.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/unigene.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/pknotsrg.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/aaindex.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/fastq.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/foldalign.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_fasta.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/infernal.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/stride.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gff.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/record_finder.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/pdb.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/stockholm.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cigar.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/phylip.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_pos.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/paml_matrix.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/pfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cmfinder.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_taxonomy.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/genbank.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/dynalign.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/unafold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rna_fold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/sprinzl.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/nupack.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/comrna.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/carnac.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnaforester.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/blast.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/column.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/mothur.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ct.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rdb.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/knetfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/tinyseq.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gibbs.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/table.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/blast_xml.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/mfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/consan.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/fasta.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/nexus.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/flowgram_collection.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/meme.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/sequence.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cutg.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/bowtie.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/paml.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ebi.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/psl.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cut.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/sfold.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/record.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/newick.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/mage.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/tree_space.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/least_squares.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/maximum_likelihood.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/distance.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/consensus.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/nj.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/tree_collection.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/calculation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/scope.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/setting.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/definition.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/markov.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/analysis.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/searchpath.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/sequence_generators.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/randomization.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/microarray_normalize.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/usage.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/microarray.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/tree.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/birth_death.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/manipulation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/annotation.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/rna2d.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/asa.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/dihedral.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/knots.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/contact.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/selection.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/pairs_util.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/misc.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/transform.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/table.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/dict_array.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/update_version.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/unit_test.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/trie.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/warning.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/dict2d.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/organizer.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/recode_alignment.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/terminal.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/option_parsing.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/array.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/parallel.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/checkpointing.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/progress_display.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/datatypes.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util copying cogent/util/modules.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util running build_ext building 'cogent.align._compare' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align 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 cogent/align/_compare.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_compare.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_compare.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_compare.so building 'cogent.align._pairwise_seqs' 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 cogent/align/_pairwise_seqs.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_seqs.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_seqs.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_seqs.so building 'cogent.align._pairwise_pogs' 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 cogent/align/_pairwise_pogs.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_pogs.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_pogs.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_pogs.so building 'cogent.evolve._solved_models' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve 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 cogent/evolve/_solved_models.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_solved_models.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_solved_models.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_solved_models.so building 'cogent.evolve._likelihood_tree' 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 cogent/evolve/_likelihood_tree.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_likelihood_tree.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_likelihood_tree.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_likelihood_tree.so building 'cogent.evolve._pairwise_distance' 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 cogent/evolve/_pairwise_distance.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_pairwise_distance.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 cogent/evolve/_pairwise_distance.c:579: /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/cogent/evolve/_pairwise_distance.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_pairwise_distance.so building 'cogent.struct._asa' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct 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 cogent/struct/_asa.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/_asa.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 cogent/struct/_asa.c:579: /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/cogent/struct/_asa.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/_asa.so building 'cogent.struct._contact' 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 cogent/struct/_contact.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/_contact.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 cogent/struct/_contact.c:579: /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/cogent/struct/_contact.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/_contact.so building 'cogent.maths._period' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths 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 cogent/maths/_period.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/_period.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 cogent/maths/_period.c:579: /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/cogent/maths/_period.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/_period.so building 'cogent.maths.spatial.ckd3' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/spatial 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 cogent/maths/spatial/ckd3.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/spatial/ckd3.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 cogent/maths/spatial/ckd3.c:579: /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/cogent/maths/spatial/ckd3.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/spatial/ckd3.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> pycogent-1.9_1 depends on package: py27-numpy>0 - found ===> pycogent-1.9_1 depends on package: py27-sphinx>=0 - found ===> pycogent-1.9_1 depends on package: py27-sqlalchemy10>=1.0.13 - found ===> pycogent-1.9_1 depends on package: py27-setuptools>0 - found ===> pycogent-1.9_1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for pycogent-1.9_1 ===> Generating temporary packing list running install running build running build_py running build_ext running install_lib creating /construction/biology/pycogent/stage/usr/local/lib/python2.7 creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster/nmds.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster/goodness_of_fit.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster/metric_scaling.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster/UPGMA.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster/approximate_mds.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/cluster/procrustes.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/_period.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix_logarithm.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/simannealingoptimiser.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix_exponential_integration.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix_exponentiation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/solve.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/optimisers.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/function_optimisation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/matrix/distance.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/scipy_optimize.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/scipy_optimisers.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/svd.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/information_criteria.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/histogram.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/jackknife.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/alpha_diversity.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/period.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai/get_by_cai.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/cai/adaptor.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/distribution.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/kendall.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/rarefaction.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/special.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/test.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/stats/ks.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/markov.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/spatial/ckd3.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/spatial/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/distance_transform.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/unifrac/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/unifrac/fast_unifrac.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/unifrac/fast_tree.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/period.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/fit_function.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/maths/geometry.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/pandaseq.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/cdbfasta.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/rnaalifold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/dialign.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/pfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/comrna.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/blast.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/cmfinder.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/parsinsert.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/raxml_v730.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/nupack.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/dotur.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/unafold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/seqprep.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/fasttree_v1.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/fastq_join.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/raxml.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/stride.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/rdp_classifier20.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/rnashapes.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/muscle_v38.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/ilm.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/usearch.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/knetfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/pplacer.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/parameters.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/gctmpca.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/mfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/blat.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/infernal.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/vienna_package.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/cd_hit.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/flash.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/clustalw.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/clearcut.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/uclust.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/contrafold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/mafft.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/carnac.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/foldalign.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/pknotsrg.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/guppy.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/muscle.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/rtax.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/rdp_classifier.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/rnaforester.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/dynalign.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/sfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/rnaview.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/formatdb.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/cove.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/mothur.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/msms.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/fasttree.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/consan.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/sfffile.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/sffinfo.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/app/bwa.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_compare.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_seqs.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/_pairwise_pogs.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/pycompare.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/dp_calculation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/indel_model.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/indel_positions.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/traceback.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/weights/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/weights/methods.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/weights/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/pairwise.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/align.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/algorithm.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/align/progressive.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/linear.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/dendrogram.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/dotplot.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/codon_usage.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/compatibility.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/arrow_rates.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/fancy_arrow.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/dinuc.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/distribution_plots.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/rlg2mpl.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/legend.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/draw/multivariate_plot.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/distance.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/tree_collection.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/maximum_likelihood.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/nj.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/least_squares.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/consensus.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/tree_space.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/phylo/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/tree.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/fasta.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/tinyseq.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/aaindex.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/foldalign.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/mothur.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/tree_xml.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/cut.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/consan.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/pfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/nupack.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/greengenes.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/unigene.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/dialign.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rdb.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/table.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/record.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/ncbi_taxonomy.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rna_fold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rnaalifold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/sfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/cutg.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/carnac.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/blast.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/column.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/gcg.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/locuslink.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/gibbs.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/meme.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/ilm.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/gff.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/kegg_taxonomy.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/stockholm.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/kegg_pos.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/knetfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/contrafold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/agilent_microarray.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/structure.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/cove.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/paml.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/cmfinder.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/mfold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/dotur.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/binary_sff.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/pknotsrg.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/gbseq.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/cigar.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/record_finder.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/bowtie.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/sprinzl.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rnashapes.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/paml_matrix.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rnaview.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/phylip.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/ebi.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/blast_xml.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/stride.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rfam.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rnaforester.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/macsim.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/sequence.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/infernal.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/flowgram_collection.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/mage.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/dynalign.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/newick.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/rna_plot.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/illumina_sequence.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/hmmscan.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/kegg_ko.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/kegg_fasta.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/clustal.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/ct.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/msms.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/psl.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/genbank.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/bpseq.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/unafold.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/flowgram.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/flowgram_parser.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/comrna.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/pdb.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/fastq.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/parse/nexus.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/misc.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/checkpointing.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/dict_array.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/update_version.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/modules.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/recode_alignment.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/table.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/trie.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/terminal.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/warning.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/dict2d.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/array.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/datatypes.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/parallel.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/progress_display.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/organizer.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/option_parsing.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/transform.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/util/unit_test.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/_asa.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/_contact.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/rna2d.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/pairs_util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/dihedral.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/knots.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/asa.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/annotation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/selection.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/contact.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/struct/manipulation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/bitvector.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/entity.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/alignment.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/tree.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/profile.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/genetic_code.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/location.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/moltype.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/usage.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/sequence.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/info.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/annotation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/core/alphabet.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/rfam.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/pdb.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ncbi.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/name.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/region.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/database.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/assembly.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/compara.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/sequence.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/species.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/genome.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/feature_level.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/host.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/db/ensembl/related_region.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data/molecular_weight.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data/energy_params.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data/nucleic_properties.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data/ligand_properties.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/data/protein_properties.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_likelihood_tree.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_pairwise_distance.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/_solved_models.so -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/solved_models.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/models.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/substitution_model.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/simulate.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/likelihood_function.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/discrete_markov.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/motif_prob_model.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/parameter_controller.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/coevolution.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/pairwise_distance.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/likelihood_tree.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/predicate.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/likelihood_calculation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/best_likelihood.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/substitution_calculation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/evolve/bootstrap.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/motif/util.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/motif/k_word.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/motif/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation/scope.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation/definition.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation/setting.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/recalculation/calculation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/text_tree.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/motif.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/fasta.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/clustal.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/bedgraph.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/alignment.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/structure.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/phylip.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/xyzrn.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/nexus.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/pdb.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/stockholm.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/rna_struct.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/table.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/mage.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/format/pdb_color.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/randomization.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/analysis.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/microarray_normalize.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/searchpath.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/microarray.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/usage.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/tree.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/sequence_generators.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/birth_death.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/cogent/seqsim/markov.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/nmds.py to nmds.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/goodness_of_fit.py to goodness_of_fit.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/metric_scaling.py to metric_scaling.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/UPGMA.py to UPGMA.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/approximate_mds.py to approximate_mds.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/procrustes.py to procrustes.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix_logarithm.py to matrix_logarithm.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/simannealingoptimiser.py to simannealingoptimiser.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix_exponential_integration.py to matrix_exponential_integration.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix_exponentiation.py to matrix_exponentiation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/solve.py to solve.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/optimisers.py to optimisers.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/function_optimisation.py to function_optimisation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix/distance.py to distance.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/scipy_optimize.py to scipy_optimize.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/scipy_optimisers.py to scipy_optimisers.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/svd.py to svd.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/information_criteria.py to information_criteria.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/histogram.py to histogram.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/jackknife.py to jackknife.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/alpha_diversity.py to alpha_diversity.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/period.py to period.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/get_by_cai.py to get_by_cai.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/adaptor.py to adaptor.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/distribution.py to distribution.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/kendall.py to kendall.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/rarefaction.py to rarefaction.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/special.py to special.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/test.py to test.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/ks.py to ks.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/markov.py to markov.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/distance_transform.py to distance_transform.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac/fast_unifrac.py to fast_unifrac.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac/fast_tree.py to fast_tree.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/period.py to period.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/fit_function.py to fit_function.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/geometry.py to geometry.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pandaseq.py to pandaseq.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cdbfasta.py to cdbfasta.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnaalifold.py to rnaalifold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/dialign.py to dialign.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pfold.py to pfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/comrna.py to comrna.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/blast.py to blast.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cmfinder.py to cmfinder.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/parsinsert.py to parsinsert.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/raxml_v730.py to raxml_v730.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/nupack.py to nupack.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/dotur.py to dotur.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/unafold.py to unafold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/seqprep.py to seqprep.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/fasttree_v1.py to fasttree_v1.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/fastq_join.py to fastq_join.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/raxml.py to raxml.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/stride.py to stride.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rdp_classifier20.py to rdp_classifier20.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnashapes.py to rnashapes.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/muscle_v38.py to muscle_v38.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/ilm.py to ilm.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/usearch.py to usearch.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/knetfold.py to knetfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pplacer.py to pplacer.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/parameters.py to parameters.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/gctmpca.py to gctmpca.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/mfold.py to mfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/blat.py to blat.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/infernal.py to infernal.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/vienna_package.py to vienna_package.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cd_hit.py to cd_hit.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/flash.py to flash.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/clustalw.py to clustalw.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/clearcut.py to clearcut.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/uclust.py to uclust.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/contrafold.py to contrafold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/mafft.py to mafft.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/carnac.py to carnac.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/foldalign.py to foldalign.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pknotsrg.py to pknotsrg.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/guppy.py to guppy.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/muscle.py to muscle.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rtax.py to rtax.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rdp_classifier.py to rdp_classifier.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnaforester.py to rnaforester.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/dynalign.py to dynalign.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/sfold.py to sfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnaview.py to rnaview.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/formatdb.py to formatdb.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cove.py to cove.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/mothur.py to mothur.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/msms.py to msms.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/fasttree.py to fasttree.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/consan.py to consan.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/sfffile.py to sfffile.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/sffinfo.py to sffinfo.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/bwa.py to bwa.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/pycompare.py to pycompare.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/dp_calculation.py to dp_calculation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/indel_model.py to indel_model.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/indel_positions.py to indel_positions.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/traceback.py to traceback.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights/methods.py to methods.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/pairwise.py to pairwise.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/align.py to align.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/algorithm.py to algorithm.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/progressive.py to progressive.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/linear.py to linear.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/dendrogram.py to dendrogram.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/dotplot.py to dotplot.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/codon_usage.py to codon_usage.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/compatibility.py to compatibility.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/arrow_rates.py to arrow_rates.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/fancy_arrow.py to fancy_arrow.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/dinuc.py to dinuc.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/distribution_plots.py to distribution_plots.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/rlg2mpl.py to rlg2mpl.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/legend.py to legend.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/multivariate_plot.py to multivariate_plot.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/distance.py to distance.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/tree_collection.py to tree_collection.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/maximum_likelihood.py to maximum_likelihood.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/nj.py to nj.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/least_squares.py to least_squares.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/consensus.py to consensus.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/tree_space.py to tree_space.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/tree.py to tree.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/fasta.py to fasta.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/tinyseq.py to tinyseq.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/aaindex.py to aaindex.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/foldalign.py to foldalign.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/mothur.py to mothur.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/tree_xml.py to tree_xml.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cut.py to cut.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/consan.py to consan.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/pfold.py to pfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/nupack.py to nupack.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/greengenes.py to greengenes.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/unigene.py to unigene.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/dialign.py to dialign.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rdb.py to rdb.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/table.py to table.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/record.py to record.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ncbi_taxonomy.py to ncbi_taxonomy.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rna_fold.py to rna_fold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnaalifold.py to rnaalifold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/sfold.py to sfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cutg.py to cutg.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/carnac.py to carnac.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/blast.py to blast.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/column.py to column.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gcg.py to gcg.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/locuslink.py to locuslink.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gibbs.py to gibbs.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/meme.py to meme.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ilm.py to ilm.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gff.py to gff.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_taxonomy.py to kegg_taxonomy.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/stockholm.py to stockholm.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_pos.py to kegg_pos.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/knetfold.py to knetfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/contrafold.py to contrafold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/agilent_microarray.py to agilent_microarray.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/structure.py to structure.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cove.py to cove.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/paml.py to paml.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cmfinder.py to cmfinder.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/mfold.py to mfold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/dotur.py to dotur.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/binary_sff.py to binary_sff.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/pknotsrg.py to pknotsrg.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gbseq.py to gbseq.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cigar.py to cigar.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/record_finder.py to record_finder.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/bowtie.py to bowtie.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/sprinzl.py to sprinzl.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnashapes.py to rnashapes.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/paml_matrix.py to paml_matrix.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnaview.py to rnaview.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/phylip.py to phylip.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ebi.py to ebi.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/blast_xml.py to blast_xml.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/stride.py to stride.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rfam.py to rfam.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnaforester.py to rnaforester.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/macsim.py to macsim.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/sequence.py to sequence.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/infernal.py to infernal.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/flowgram_collection.py to flowgram_collection.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/mage.py to mage.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/dynalign.py to dynalign.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/newick.py to newick.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rna_plot.py to rna_plot.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/illumina_sequence.py to illumina_sequence.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/hmmscan.py to hmmscan.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_ko.py to kegg_ko.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_fasta.py to kegg_fasta.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/clustal.py to clustal.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ct.py to ct.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/msms.py to msms.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/psl.py to psl.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/genbank.py to genbank.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/bpseq.py to bpseq.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/unafold.py to unafold.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/flowgram.py to flowgram.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/flowgram_parser.py to flowgram_parser.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/comrna.py to comrna.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/pdb.py to pdb.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/fastq.py to fastq.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/nexus.py to nexus.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/misc.py to misc.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/checkpointing.py to checkpointing.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/dict_array.py to dict_array.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/update_version.py to update_version.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/modules.py to modules.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/recode_alignment.py to recode_alignment.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/table.py to table.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/trie.py to trie.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/terminal.py to terminal.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/warning.py to warning.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/dict2d.py to dict2d.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/array.py to array.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/datatypes.py to datatypes.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/parallel.py to parallel.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/progress_display.py to progress_display.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/organizer.py to organizer.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/option_parsing.py to option_parsing.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/transform.py to transform.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/unit_test.py to unit_test.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/rna2d.py to rna2d.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/pairs_util.py to pairs_util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/dihedral.py to dihedral.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/knots.py to knots.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/asa.py to asa.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/annotation.py to annotation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/selection.py to selection.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/contact.py to contact.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/manipulation.py to manipulation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/bitvector.py to bitvector.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/entity.py to entity.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/alignment.py to alignment.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/tree.py to tree.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/profile.py to profile.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/genetic_code.py to genetic_code.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/location.py to location.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/moltype.py to moltype.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/usage.py to usage.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/sequence.py to sequence.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/info.py to info.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/annotation.py to annotation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/alphabet.py to alphabet.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/rfam.py to rfam.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/pdb.py to pdb.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ncbi.py to ncbi.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/name.py to name.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/region.py to region.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/database.py to database.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/assembly.py to assembly.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/compara.py to compara.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/sequence.py to sequence.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/species.py to species.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/genome.py to genome.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/feature_level.py to feature_level.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/host.py to host.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/related_region.py to related_region.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/molecular_weight.py to molecular_weight.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/energy_params.py to energy_params.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/nucleic_properties.py to nucleic_properties.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/ligand_properties.py to ligand_properties.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/protein_properties.py to protein_properties.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/solved_models.py to solved_models.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/models.py to models.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/substitution_model.py to substitution_model.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/simulate.py to simulate.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/likelihood_function.py to likelihood_function.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/discrete_markov.py to discrete_markov.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/motif_prob_model.py to motif_prob_model.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/parameter_controller.py to parameter_controller.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/coevolution.py to coevolution.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/pairwise_distance.py to pairwise_distance.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/likelihood_tree.py to likelihood_tree.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/predicate.py to predicate.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/likelihood_calculation.py to likelihood_calculation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/best_likelihood.py to best_likelihood.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/substitution_calculation.py to substitution_calculation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/bootstrap.py to bootstrap.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif/util.py to util.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif/k_word.py to k_word.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/scope.py to scope.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/definition.py to definition.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/setting.py to setting.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/calculation.py to calculation.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/text_tree.py to text_tree.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/motif.py to motif.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/fasta.py to fasta.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/clustal.py to clustal.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/bedgraph.py to bedgraph.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/alignment.py to alignment.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/structure.py to structure.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/phylip.py to phylip.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/xyzrn.py to xyzrn.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/nexus.py to nexus.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/pdb.py to pdb.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/stockholm.py to stockholm.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/rna_struct.py to rna_struct.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/table.py to table.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/mage.py to mage.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/pdb_color.py to pdb_color.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/randomization.py to randomization.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/__init__.py to __init__.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/analysis.py to analysis.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/microarray_normalize.py to microarray_normalize.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/searchpath.py to searchpath.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/microarray.py to microarray.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/usage.py to usage.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/tree.py to tree.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/sequence_generators.py to sequence_generators.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/birth_death.py to birth_death.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/markov.py to markov.pyc writing byte-compilation script '/tmp/tmpINP0Da.py' /usr/local/bin/python2.7 -O /tmp/tmpINP0Da.py removing /tmp/tmpINP0Da.py running install_egg_info running egg_info creating cogent.egg-info writing requirements to cogent.egg-info/requires.txt writing cogent.egg-info/PKG-INFO writing top-level names to cogent.egg-info/top_level.txt writing dependency_links to cogent.egg-info/dependency_links.txt writing manifest file 'cogent.egg-info/SOURCES.txt' reading manifest file 'cogent.egg-info/SOURCES.txt' writing manifest file 'cogent.egg-info/SOURCES.txt' Copying cogent.egg-info to /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent-1.9-py2.7.egg-info running install_scripts writing list of installed files to '/construction/biology/pycogent/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for pycogent-1.9_1 file sizes/checksums [1065]: .......... done packing files [1065]: .......... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 20 JUL 2018 at 23:32:34 UTC Duration: 00:01:35