=> Building biology/pycogent@py27 Started : Friday, 24 JAN 2020 at 03:52:17 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1284.g34ca1-DEVELOPMENT #20: Fri Jan 17 02:50:51 PST 2020 root@sting.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.7-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.7-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=gcc80 -------------------------------------------------- -- 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=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/pycogent/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.7 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=LiveSystem 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=15 DPORTS_BUILDER= yes DISABLE_LICENSES= yes DEFAULT_VERSIONS= ssl=openssl FORCE_PACKAGE= yes DEVELOPER= yes HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.30.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500709 OSVERSION=9999999 OSREL=5.7 _OSRELEASE=5.7-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained, uses EOLed python27. It is scheduled to be removed on or after 2020-01-27. -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> pycogent-1.9_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz Installing pkg-1.12.0... Extracting pkg-1.12.0: .......... done ===> pycogent-1.9_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pycogent-1.9_3 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained, uses EOLed python27. It is scheduled to be removed on or after 2020-01-27. => pycogent-pycogent-1.9_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/pycogent/pycogent/tar.gz/1.9?dummy=/pycogent-pycogent-1.9_GH0.tar.gz fetch: https://codeload.github.com/pycogent/pycogent/tar.gz/1.9?dummy=/pycogent-pycogent-1.9_GH0.tar.gz: size unknown fetch: https://codeload.github.com/pycogent/pycogent/tar.gz/1.9?dummy=/pycogent-pycogent-1.9_GH0.tar.gz: size of remote file is not known pycogent-pycogent-1.9_GH0.tar.gz 3656 kB 6297 kBps 00s ===> Fetching all distfiles required by pycogent-1.9_3 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained, uses EOLed python27. It is scheduled to be removed on or after 2020-01-27. ===> Fetching all distfiles required by pycogent-1.9_3 for building => SHA256 Checksum OK for pycogent-pycogent-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained, uses EOLed python27. It is scheduled to be removed on or after 2020-01-27. ===> Fetching all distfiles required by pycogent-1.9_3 for building ===> Extracting for pycogent-1.9_3 => SHA256 Checksum OK for pycogent-pycogent-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for pycogent-1.9_3 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> pycogent-1.9_3 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.16.5_3,1.txz Installing py27-numpy-1.16.5_3,1... `-- Installing gcc8-8.3.0_3... | `-- Installing binutils-2.33.1_2,1... | | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: . done | | `-- Extracting gettext-runtime-0.20.1: .......... done | `-- Extracting binutils-2.33.1_2,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ...... done `-- Extracting gcc8-8.3.0_3: .......... done `-- Installing openblas-0.3.7,1... `-- Extracting openblas-0.3.7,1: .......... done `-- Installing py27-setuptools-44.0.0... | `-- Installing python27-2.7.17_1... | | `-- Installing expat-2.2.8... | | `-- Extracting expat-2.2.8: .......... done | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | | `-- Installing openssl-1.1.1d,1... | | `-- Extracting openssl-1.1.1d,1: .......... done | | `-- Installing readline-8.0.1... | | `-- Extracting readline-8.0.1: .......... done | `-- Extracting python27-2.7.17_1: .......... done `-- Extracting py27-setuptools-44.0.0: .......... done `-- Installing suitesparse-5.4.0_4... | `-- Installing metis-5.1.0_8... | `-- Extracting metis-5.1.0_8: .......... done | `-- Installing tbb-2020.0... | `-- Extracting tbb-2020.0: .......... done `-- Extracting suitesparse-5.4.0_4: .......... done Extracting py27-numpy-1.16.5_3,1: .......... done ===== Message from gcc8-8.3.0_3: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python27-2.7.17_1: -- 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 -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===== Message from py27-setuptools-44.0.0: -- Only /usr/local/bin/easy_install-2.7 script has been installed since Python 2.7 is not the default Python version. ===> pycogent-1.9_3 depends on package: py27-numpy>0 - found ===> Returning to build of pycogent-1.9_3 ===> pycogent-1.9_3 depends on package: py27-sphinx>=0 - not found ===> Installing existing package /packages/All/py27-sphinx-1.6.5_2,1.txz Installing py27-sphinx-1.6.5_2,1... `-- Installing ca_root_nss-3.49.1... `-- Extracting ca_root_nss-3.49.1: ..... done `-- Installing py27-Babel-2.7.0... | `-- Installing py27-pytz-2019.3,1... | `-- Extracting py27-pytz-2019.3,1: .......... done `-- Extracting py27-Babel-2.7.0: .......... done `-- Installing py27-Jinja2-2.10.1... | `-- Installing py27-MarkupSafe-1.1.1... | `-- Extracting py27-MarkupSafe-1.1.1: .......... done `-- Extracting py27-Jinja2-2.10.1: .......... done `-- Installing py27-alabaster-0.7.6... `-- Extracting py27-alabaster-0.7.6: .......... done `-- Installing py27-docutils-0.15.2... `-- Extracting py27-docutils-0.15.2: .......... done `-- Installing py27-imagesize-1.1.0... `-- Extracting py27-imagesize-1.1.0: ....... done `-- Installing py27-pygments-2.5.2... `-- Extracting py27-pygments-2.5.2: .......... done `-- Installing py27-requests-2.22.0... | `-- Installing py27-certifi-2019.11.28... | `-- Extracting py27-certifi-2019.11.28: .......... done | `-- Installing py27-chardet-3.0.4_3... | `-- Extracting py27-chardet-3.0.4_3: .......... done | `-- Installing py27-idna-2.8... | `-- Extracting py27-idna-2.8: .......... done | `-- Installing py27-urllib3-1.25.7,1... | | `-- Installing py27-cryptography-2.6.1... | | `-- Installing py27-asn1crypto-0.24.0... | | `-- Extracting py27-asn1crypto-0.24.0: .......... done | | `-- Installing py27-cffi-1.13.2... | | | `-- Installing py27-pycparser-2.19... | | | `-- Extracting py27-pycparser-2.19: .......... done | | `-- Extracting py27-cffi-1.13.2: .......... done | | `-- Installing py27-enum34-1.1.6... | | `-- Extracting py27-enum34-1.1.6: .......... done | | `-- Installing py27-ipaddress-1.0.23... | | `-- Extracting py27-ipaddress-1.0.23: ....... done | | `-- Installing py27-six-1.13.0... | | `-- Extracting py27-six-1.13.0: ....... done | | `-- Extracting py27-cryptography-2.6.1: .......... done | | `-- Installing py27-openssl-19.0.0... | | `-- Extracting py27-openssl-19.0.0: .......... done | | `-- Installing py27-pysocks-1.7.1... | | `-- Extracting py27-pysocks-1.7.1: .......... done | `-- Extracting py27-urllib3-1.25.7,1: .......... done `-- Extracting py27-requests-2.22.0: .......... done `-- Installing py27-snowballstemmer-1.2.1... | `-- Installing py27-pystemmer-1.3.0_2... | `-- Extracting py27-pystemmer-1.3.0_2: ..... done `-- Extracting py27-snowballstemmer-1.2.1: .......... done `-- Installing py27-sphinx_rtd_theme-0.4.3... `-- Extracting py27-sphinx_rtd_theme-0.4.3: .......... done `-- Installing py27-sphinxcontrib-websupport-1.1.2... `-- Extracting py27-sphinxcontrib-websupport-1.1.2: .......... done `-- Installing py27-typing-3.7.4... `-- Extracting py27-typing-3.7.4: ....... done Extracting py27-sphinx-1.6.5_2,1: .......... done ===== Message from ca_root_nss-3.49.1: -- 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. 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-urllib3-1.25.7,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===> pycogent-1.9_3 depends on package: py27-sphinx>=0 - found ===> Returning to build of pycogent-1.9_3 ===> pycogent-1.9_3 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-sqlite3-2.7.17_7... | `-- Installing sqlite3-3.30.1... | `-- Extracting sqlite3-3.30.1: ......... done `-- Extracting py27-sqlite3-2.7.17_7: ..... done Extracting py27-sqlalchemy10-1.0.14: .......... done ===> pycogent-1.9_3 depends on package: py27-sqlalchemy10>=1.0.13 - found ===> Returning to build of pycogent-1.9_3 ===> pycogent-1.9_3 depends on executable: cython-2.7 - not found ===> Installing existing package /packages/All/py27-cython-0.29.13_1.txz Installing py27-cython-0.29.13_1... Extracting py27-cython-0.29.13_1: .......... done ===> pycogent-1.9_3 depends on executable: cython-2.7 - found ===> Returning to build of pycogent-1.9_3 ===> pycogent-1.9_3 depends on package: py27-setuptools>0 - found ===> pycogent-1.9_3 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for pycogent-1.9_3 /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/pycogent/pycogent-1.9/cogent/evolve/_pairwise_distance.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/pycogent/pycogent-1.9/cogent/maths/_period.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/pycogent/pycogent-1.9/cogent/maths/spatial/ckd3.pxd tree = Parsing.p_module(s, pxd, full_module_name) 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' /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/pycogent/pycogent-1.9/cogent/struct/_asa.pxd tree = Parsing.p_module(s, pxd, full_module_name) 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' /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/biology/pycogent/pycogent-1.9/cogent/struct/_contact.pxd tree = Parsing.p_module(s, pxd, full_module_name) 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_3 running build running build_py creating build creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7 creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent copying cogent/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/progressive.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/dp_calculation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/align.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/pycompare.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/indel_model.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/traceback.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/algorithm.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/indel_positions.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align copying cogent/align/pairwise.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/weights copying cogent/align/weights/methods.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/weights copying cogent/align/weights/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/weights copying cogent/align/weights/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/weights creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/seqprep.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/stride.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnaforester.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/usearch.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/sfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/contrafold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/parsinsert.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/clustalw.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/vienna_package.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/blat.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rdp_classifier20.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/fastq_join.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/infernal.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/muscle_v38.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/ilm.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pknotsrg.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/dotur.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnaalifold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/msms.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/foldalign.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cd_hit.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/fasttree_v1.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/guppy.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pplacer.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnaview.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/muscle.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/formatdb.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/dialign.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/clearcut.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/blast.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/dynalign.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cdbfasta.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/parameters.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/bwa.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/raxml.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cmfinder.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/raxml_v730.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/sfffile.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/gctmpca.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/comrna.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/uclust.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/mfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/flash.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/mothur.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rnashapes.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/fasttree.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/consan.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/nupack.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/knetfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/pandaseq.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/cove.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rdp_classifier.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/mafft.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/unafold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/carnac.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/sffinfo.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app copying cogent/app/rtax.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/app creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/nmds.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/UPGMA.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/metric_scaling.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/approximate_mds.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/procrustes.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster copying cogent/cluster/goodness_of_fit.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/cluster creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/annotation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/alphabet.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/moltype.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/entity.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/location.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/sequence.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/usage.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/tree.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/alignment.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/genetic_code.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/info.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/profile.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core copying cogent/core/bitvector.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/core creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/data copying cogent/data/ligand_properties.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/data copying cogent/data/nucleic_properties.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/data copying cogent/data/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/data copying cogent/data/molecular_weight.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/data copying cogent/data/protein_properties.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/data copying cogent/data/energy_params.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/data creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db copying cogent/db/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db copying cogent/db/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db copying cogent/db/ncbi.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db copying cogent/db/rfam.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db copying cogent/db/pdb.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/host.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/related_region.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/region.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/genome.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/name.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/compara.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/species.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/assembly.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/database.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/feature_level.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/sequence.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ensembl creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/dendrogram.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/dinuc.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/distribution_plots.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/fancy_arrow.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/legend.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/multivariate_plot.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/rlg2mpl.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/arrow_rates.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/linear.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/codon_usage.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/compatibility.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/dotplot.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw copying cogent/draw/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/discrete_markov.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_calculation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_tree.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/predicate.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/coevolution.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/parameter_controller.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/solved_models.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_function.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/motif_prob_model.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/pairwise_distance.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/simulate.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/bootstrap.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/substitution_model.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/substitution_calculation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/models.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve copying cogent/evolve/best_likelihood.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/stockholm.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/nexus.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/rna_struct.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/alignment.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/clustal.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/text_tree.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/bedgraph.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/pdb.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/phylip.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/motif.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/fasta.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/mage.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/pdb_color.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/structure.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/table.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format copying cogent/format/xyzrn.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/distance_transform.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/solve.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/markov.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/period.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/scipy_optimize.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/matrix_exponential_integration.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/geometry.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/scipy_optimisers.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/optimisers.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/simannealingoptimiser.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/matrix_logarithm.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/fit_function.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/matrix_exponentiation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/svd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/function_optimisation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths copying cogent/maths/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/matrix copying cogent/maths/matrix/distance.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/matrix copying cogent/maths/matrix/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/matrix creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/test.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/ks.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/kendall.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/jackknife.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/distribution.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/information_criteria.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/special.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/alpha_diversity.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/histogram.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/period.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/rarefaction.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/adaptor.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/get_by_cai.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/stats/cai creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_unifrac.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_tree.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/unifrac creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/spatial copying cogent/maths/spatial/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/spatial creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/motif copying cogent/motif/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/motif copying cogent/motif/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/motif copying cogent/motif/k_word.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/motif creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/table.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/carnac.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/agilent_microarray.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/aaindex.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/paml.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rfam.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/flowgram_collection.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/hmmscan.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/unigene.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_pos.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gff.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/unafold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/bowtie.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cmfinder.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_ko.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/locuslink.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/bpseq.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/pknotsrg.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/nexus.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/greengenes.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/record.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/newick.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cove.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/dialign.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/pfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gbseq.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cigar.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ncbi_taxonomy.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/blast_xml.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/knetfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/foldalign.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/blast.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/psl.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/column.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ilm.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/msms.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rna_fold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/consan.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/infernal.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/stride.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ct.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/clustal.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/mfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnaview.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/fasta.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/flowgram_parser.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/tinyseq.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/dynalign.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gibbs.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/gcg.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/sequence.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/ebi.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/sfold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/macsim.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/genbank.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/paml_matrix.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/phylip.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnaalifold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/illumina_sequence.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnashapes.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/structure.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/dotur.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cutg.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rnaforester.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/comrna.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/pdb.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_taxonomy.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/sprinzl.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/fastq.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rdb.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/stockholm.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/cut.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/meme.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/record_finder.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/kegg_fasta.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/mothur.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/flowgram.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/tree.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/binary_sff.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/rna_plot.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/tree_xml.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/mage.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/contrafold.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse copying cogent/parse/nupack.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/parse creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/tree_space.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/consensus.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/distance.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/nj.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/tree_collection.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/maximum_likelihood.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/least_squares.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo copying cogent/phylo/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/phylo creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/definition.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/calculation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/scope.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/recalculation copying cogent/recalculation/setting.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/recalculation creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/searchpath.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/sequence_generators.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/analysis.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/microarray.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/birth_death.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/tree.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/randomization.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/markov.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/microarray_normalize.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim copying cogent/seqsim/usage.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/seqsim creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/manipulation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/dihedral.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/asa.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/contact.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/pairs_util.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/selection.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/knots.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/annotation.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct copying cogent/struct/rna2d.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct creating build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/table.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/transform.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/progress_display.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/dict2d.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/organizer.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/array.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/parallel.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/update_version.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/option_parsing.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/misc.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/dict_array.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/checkpointing.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/trie.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/modules.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/datatypes.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/terminal.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/recode_alignment.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/warning.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util copying cogent/util/unit_test.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/util running build_ext building 'cogent.align._compare' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent creating build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-SYNTH-x86_64-2.7/cogent/align/_compare.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/_compare.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/_compare.so building 'cogent.align._pairwise_seqs' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-SYNTH-x86_64-2.7/cogent/align/_pairwise_seqs.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/_pairwise_seqs.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/_pairwise_seqs.so building 'cogent.align._pairwise_pogs' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-SYNTH-x86_64-2.7/cogent/align/_pairwise_pogs.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/_pairwise_pogs.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/align/_pairwise_pogs.so building 'cogent.evolve._solved_models' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-SYNTH-x86_64-2.7/cogent/evolve/_solved_models.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve/_solved_models.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve/_solved_models.so building 'cogent.evolve._likelihood_tree' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-SYNTH-x86_64-2.7/cogent/evolve/_likelihood_tree.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve/_likelihood_tree.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve/_likelihood_tree.so building 'cogent.evolve._pairwise_distance' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-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:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/evolve/_pairwise_distance.c:611: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve/_pairwise_distance.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve/_pairwise_distance.so building 'cogent.struct._asa' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-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:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_asa.c:611: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct/_asa.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct/_asa.so building 'cogent.struct._contact' extension cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-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:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_contact.c:611: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct/_contact.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/struct/_contact.so building 'cogent.maths._period' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-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:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/_period.c:611: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/_period.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/_period.so building 'cogent.maths.spatial.ckd3' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/spatial cc -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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-5.7-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:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/spatial/ckd3.c:611: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/spatial/ckd3.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/spatial/ckd3.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> pycogent-1.9_3 depends on package: py27-numpy>0 - found ===> pycogent-1.9_3 depends on package: py27-sphinx>=0 - found ===> pycogent-1.9_3 depends on package: py27-sqlalchemy10>=1.0.13 - found ===> pycogent-1.9_3 depends on package: py27-setuptools>0 - found ===> pycogent-1.9_3 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for pycogent-1.9_3 ===> 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/align copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/align/algorithm.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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/align/traceback.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/align/progressive.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/align/pairwise.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/format copying build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/format/pdb_color.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/format/fasta.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/core copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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/struct copying build/lib.dragonfly-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/struct/manipulation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/struct/annotation.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/app copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/app/bwa.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/app/clearcut.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/maths copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/maths/distance_transform.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/maths/period.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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/maths/solve.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-5.7-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-5.7-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-5.7-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-5.7-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/stats copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/maths/stats/period.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-5.7-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 creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/maths/function_optimisation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.7-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-5.7-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/unifrac copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/maths/geometry.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/maths/optimisers.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/db copying build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/db/ncbi.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/db/rfam.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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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 copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/db/pdb.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/draw copying build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/draw/multivariate_plot.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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/motif copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/motif/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif copying build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/motif/util.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/evolve copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/evolve/bootstrap.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-5.7-SYNTH-x86_64-2.7/cogent/evolve/likelihood_calculation.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/data copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/data/energy_params.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/seqsim/markov.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/seqsim/birth_death.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim creating /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/recalculation/calculation.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/recalculation/definition.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/parse copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/parse/nexus.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/parse/cmfinder.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/phylo copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/phylo/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/phylo/tree_space.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/util copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/util/unit_test.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/util/transform.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/cluster copying build/lib.dragonfly-5.7-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-5.7-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-5.7-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-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/cluster/procrustes.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-5.7-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-5.7-SYNTH-x86_64-2.7/cogent/cluster/__init__.py -> /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster 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/__init__.py to __init__.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/weights/util.py to util.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/__init__.py to __init__.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/dp_calculation.py to dp_calculation.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/indel_model.py to indel_model.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/align/indel_positions.py to indel_positions.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/format/pdb_color.py to pdb_color.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/clustal.py to clustal.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/phylip.py to phylip.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/stockholm.py to stockholm.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/alignment.py to alignment.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/text_tree.py to text_tree.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/mage.py to mage.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/structure.py to structure.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/core/alignment.py to alignment.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/entity.py to entity.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/usage.py to usage.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/sequence.py to sequence.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/info.py to info.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/bitvector.py to bitvector.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/alphabet.py to alphabet.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/struct/pairs_util.py to pairs_util.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/rna2d.py to rna2d.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/asa.py to asa.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/dihedral.py to dihedral.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/annotation.py to annotation.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/rnaview.py to rnaview.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/rdp_classifier20.py to rdp_classifier20.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/carnac.py to carnac.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/rnaforester.py to rnaforester.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/util.py to util.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/mfold.py to mfold.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/dialign.py to dialign.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/flash.py to flash.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/stride.py to stride.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/pfold.py to pfold.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/raxml.py to raxml.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/formatdb.py to formatdb.pyc byte-compiling 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/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/randomization.py to randomization.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/sequence_generators.py to sequence_generators.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_normalize.py to microarray_normalize.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/analysis.py to analysis.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/markov.py to markov.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/birth_death.py to birth_death.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/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/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/parse/rnaforester.py to rnaforester.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/msms.py to msms.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/mfold.py to mfold.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/pdb.py to pdb.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/structure.py to structure.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/__init__.py to __init__.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/dynalign.py to dynalign.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/cut.py to cut.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/sfold.py to sfold.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/nupack.py to nupack.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/stride.py to stride.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/agilent_microarray.py to agilent_microarray.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/contrafold.py to contrafold.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/cutg.py to cutg.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/dotur.py to dotur.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/kegg_ko.py to kegg_ko.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/record_finder.py to record_finder.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/unigene.py to unigene.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/flowgram_collection.py to flowgram_collection.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/genbank.py to genbank.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/sprinzl.py to sprinzl.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/rna_plot.py to rna_plot.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/illumina_sequence.py to illumina_sequence.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/gcg.py to gcg.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/psl.py to psl.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/parse/meme.py to meme.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/table.py to table.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/kegg_fasta.py to kegg_fasta.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/cigar.py to cigar.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/kegg_taxonomy.py to kegg_taxonomy.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/gibbs.py to gibbs.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/stockholm.py to stockholm.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/ct.py to ct.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/rna_fold.py to rna_fold.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/locuslink.py to locuslink.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/paml_matrix.py to paml_matrix.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/rdb.py to rdb.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/pknotsrg.py to pknotsrg.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/ncbi_taxonomy.py to ncbi_taxonomy.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/ilm.py to ilm.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/sequence.py to sequence.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/blast_xml.py to blast_xml.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/cmfinder.py to cmfinder.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/distance.py to distance.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/maximum_likelihood.py to maximum_likelihood.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/phylo/consensus.py to consensus.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/tree_space.py to tree_space.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/dict2d.py to dict2d.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/parallel.py to parallel.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/warning.py to warning.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/datatypes.py to datatypes.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/update_version.py to update_version.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/table.py to table.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/__init__.py to __init__.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/checkpointing.py to checkpointing.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/unit_test.py to unit_test.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/transform.py to transform.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/goodness_of_fit.py to goodness_of_fit.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/nmds.py to nmds.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/cluster/UPGMA.py to UPGMA.pyc byte-compiling /construction/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/__init__.py to __init__.pyc writing byte-compilation script '/tmp/tmpVkDpF7.py' /usr/local/bin/python2.7 -O /tmp/tmpVkDpF7.py removing /tmp/tmpVkDpF7.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) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python2.7/site-packages/cogent/align/_compare.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for pycogent-1.9_3 file sizes/checksums [1062]: .......... done packing files [1062]: .......... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 24 JAN 2020 at 03:54:01 UTC Duration: 00:01:44