=> Building biology/pycogent build started at Tue Oct 4 21:59:46 PDT 2016 port directory: /usr/ports/biology/pycogent building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: python@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../04//usr/ports/biology/pycogent/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=pycogent-1.9 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/biology/pycogent XDG_CONFIG_HOME=/wrkdirs/biology/pycogent HOME=/wrkdirs/biology/pycogent TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/pycogent XDG_CONFIG_HOME=/wrkdirs/biology/pycogent HOME=/wrkdirs/biology/pycogent TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" 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 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly4 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_VER=2.7 PYTHON_VERSION=python2.7 OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/pycogent" EXAMPLESDIR="share/examples/pycogent" DATADIR="share/pycogent" WWWDIR="www/pycogent" ETCDIR="etc/pycogent" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> pycogent-1.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> pycogent-1.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pycogent-1.9 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by pycogent-1.9 for building =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by pycogent-1.9 for building => SHA256 Checksum OK for pycogent-pycogent-1.9_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by pycogent-1.9 for building ===> Extracting for pycogent-1.9 => SHA256 Checksum OK for pycogent-pycogent-1.9_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for pycogent-1.9 =========================================================================== =================================================== ===> pycogent-1.9 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - not found ===> Installing existing package /packages/All/py27-numpy-1.11.1,1.txz Installing py27-numpy-1.11.1,1... `-- Installing python27-2.7.12... | `-- Installing expat-2.2.0... | `-- Extracting expat-2.2.0: .......... done | `-- Installing readline-6.3.8... | | `-- Installing indexinfo-0.2.5... | | `-- Extracting indexinfo-0.2.5: .... done | | `-- Installing ncurses-6.0_5... | | `-- Extracting ncurses-6.0_5: .......... done | `-- Extracting readline-6.3.8: .......... done | `-- Installing libffi-3.2.1... | `-- Extracting libffi-3.2.1: .......... done | `-- Installing libressl-2.4.3... | `-- Extracting libressl-2.4.3: .......... done | `-- Installing gettext-runtime-0.19.8.1... | `-- Extracting gettext-runtime-0.19.8.1: .......... done `-- Extracting python27-2.7.12: .......... done `-- Installing py27-setuptools27-23.1.0... `-- Extracting py27-setuptools27-23.1.0: .......... done `-- Installing lapack-3.5.0... | `-- Installing blas-3.5.0_3... | | `-- Installing gcc5-5.4.0... | | `-- Installing mpc-1.0.3... | | | `-- Installing gmp-5.1.3_3... | | | `-- Extracting gmp-5.1.3_3: .......... done | | | `-- Installing mpfr-3.1.5... | | | `-- Extracting mpfr-3.1.5: .......... done | | `-- Extracting mpc-1.0.3: ...... done | | `-- Installing binutils-2.27_4,1... | | `-- Extracting binutils-2.27_4,1: .......... done | | `-- Extracting gcc5-5.4.0: .......... done | `-- Extracting blas-3.5.0_3: ....... done `-- Extracting lapack-3.5.0: .......... done `-- Installing openblas-0.2.18_1,1... `-- Extracting openblas-0.2.18_1,1: ......... done `-- Installing suitesparse-4.0.2_4... `-- Extracting suitesparse-4.0.2_4: .......... done `-- Installing cblas-1.0_4... `-- Extracting cblas-1.0_4: ......... done Extracting py27-numpy-1.11.1,1: .......... done Message from ncurses-6.0_5: ===> NOTICE: The ncurses port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from python27-2.7.12: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from gcc5-5.4.0: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_4: ===> NOTICE: The cblas port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> pycogent-1.9 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - found ===> Returning to build of pycogent-1.9 ===> pycogent-1.9 depends on file: /usr/local/bin/cython - not found ===> Installing existing package /packages/All/cython-0.24.txz Installing cython-0.24... Extracting cython-0.24: .......... done ===> pycogent-1.9 depends on file: /usr/local/bin/cython - found ===> Returning to build of pycogent-1.9 ===> pycogent-1.9 depends on file: /usr/local/bin/sphinx-build - not found ===> Installing existing package /packages/All/py27-sphinx-1.4.6_1.txz Installing py27-sphinx-1.4.6_1... `-- Installing py27-snowballstemmer-1.2.0_1... | `-- Installing py27-pystemmer-1.3.0_1... | `-- Extracting py27-pystemmer-1.3.0_1: ......... done `-- Extracting py27-snowballstemmer-1.2.0_1: .......... done `-- Installing ca_root_nss-3.27... `-- Extracting ca_root_nss-3.27: ....... done `-- Installing py27-alabaster-0.7.6... `-- Extracting py27-alabaster-0.7.6: .......... done `-- Installing py27-sphinx_rtd_theme-0.1.9... `-- Extracting py27-sphinx_rtd_theme-0.1.9: .......... done `-- Installing py27-pygments-2.1.3... `-- Extracting py27-pygments-2.1.3: .......... done `-- Installing py27-docutils-0.12... `-- Extracting py27-docutils-0.12: .......... done `-- Installing py27-six-1.10.0... `-- Extracting py27-six-1.10.0: .......... done `-- Installing py27-Jinja2-2.8... | `-- Installing py27-Babel-2.3.4... | | `-- Installing py27-pytz-2016.6.1,1... | | `-- Extracting py27-pytz-2016.6.1,1: .......... done | `-- Extracting py27-Babel-2.3.4: .......... done | `-- Installing py27-MarkupSafe-0.23... | `-- Extracting py27-MarkupSafe-0.23: .......... done `-- Extracting py27-Jinja2-2.8: .......... done `-- Installing py27-imagesize-0.7.1... `-- Extracting py27-imagesize-0.7.1: .......... done Extracting py27-sphinx-1.4.6_1: .......... done Message from py27-pystemmer-1.3.0_1: ===> NOTICE: The py27-pystemmer port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from ca_root_nss-3.27: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> pycogent-1.9 depends on file: /usr/local/bin/sphinx-build - found ===> Returning to build of pycogent-1.9 ===> pycogent-1.9 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-sqlite3-2.7.12_7... | `-- Installing sqlite3-3.14.1_1... | `-- Extracting sqlite3-3.14.1_1: .......... done `-- Extracting py27-sqlite3-2.7.12_7: ........ done Extracting py27-sqlalchemy10-1.0.14: .......... done ===> pycogent-1.9 depends on package: py27-sqlalchemy10>=1.0.13 - found ===> Returning to build of pycogent-1.9 ===> pycogent-1.9 depends on package: py27-setuptools27>0 - found ===> pycogent-1.9 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for pycogent-1.9 running config =========================================================================== =================================================== ===> Building for pycogent-1.9 running build running build_py creating build creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7 creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent copying cogent/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/algorithm.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/align.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/pairwise.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/traceback.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/dp_calculation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/pycompare.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/indel_model.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/progressive.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align copying cogent/align/indel_positions.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/weights copying cogent/align/weights/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/weights copying cogent/align/weights/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/weights copying cogent/align/weights/methods.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/weights creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/dialign.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/rnaalifold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/fastq_join.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/mfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/dynalign.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/formatdb.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/ilm.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/sffinfo.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/usearch.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/parameters.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/clustalw.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/uclust.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/msms.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/clearcut.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/gctmpca.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/cd_hit.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/cmfinder.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/consan.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/rnashapes.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/pknotsrg.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/mafft.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/cove.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/parsinsert.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/pfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/foldalign.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/dotur.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/vienna_package.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/rdp_classifier20.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/cdbfasta.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/sfffile.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/rnaview.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/pandaseq.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/comrna.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/guppy.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/infernal.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/unafold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/contrafold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/fasttree_v1.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/muscle.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/carnac.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/rdp_classifier.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/stride.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/bwa.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/rtax.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/raxml.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/knetfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/muscle_v38.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/seqprep.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/blast.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/mothur.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/pplacer.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/nupack.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/raxml_v730.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/rnaforester.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/flash.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/sfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/blat.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/fasttree.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app copying cogent/app/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster copying cogent/cluster/procrustes.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster copying cogent/cluster/approximate_mds.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster copying cogent/cluster/goodness_of_fit.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster copying cogent/cluster/metric_scaling.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster copying cogent/cluster/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster copying cogent/cluster/nmds.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster copying cogent/cluster/UPGMA.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/annotation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/genetic_code.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/entity.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/moltype.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/profile.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/alphabet.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/sequence.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/bitvector.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/usage.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/location.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/info.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/alignment.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core copying cogent/core/tree.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data copying cogent/data/molecular_weight.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data copying cogent/data/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data copying cogent/data/energy_params.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data copying cogent/data/nucleic_properties.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data copying cogent/data/protein_properties.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data copying cogent/data/ligand_properties.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db copying cogent/db/rfam.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db copying cogent/db/pdb.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db copying cogent/db/ncbi.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db copying cogent/db/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db copying cogent/db/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/compara.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/sequence.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/genome.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/database.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/region.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/host.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/name.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/feature_level.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/related_region.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/assembly.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl copying cogent/db/ensembl/species.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/distribution_plots.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/arrow_rates.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/dotplot.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/fancy_arrow.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/compatibility.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/linear.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/rlg2mpl.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/dinuc.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/codon_usage.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/legend.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/dendrogram.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw copying cogent/draw/multivariate_plot.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/best_likelihood.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/motif_prob_model.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/predicate.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_tree.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/parameter_controller.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/pairwise_distance.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/simulate.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/discrete_markov.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/substitution_model.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/solved_models.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/models.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/substitution_calculation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/bootstrap.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_function.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/coevolution.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve copying cogent/evolve/likelihood_calculation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/pdb_color.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/bedgraph.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/stockholm.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/motif.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/pdb.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/clustal.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/mage.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/xyzrn.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/table.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/nexus.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/structure.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/text_tree.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/phylip.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/fasta.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/alignment.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format copying cogent/format/rna_struct.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/matrix_exponentiation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/scipy_optimize.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/svd.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/geometry.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/matrix_logarithm.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/fit_function.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/matrix_exponential_integration.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/simannealingoptimiser.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/scipy_optimisers.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/solve.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/optimisers.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/function_optimisation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/markov.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/distance_transform.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths copying cogent/maths/period.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix copying cogent/maths/matrix/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix copying cogent/maths/matrix/distance.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/information_criteria.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/kendall.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/jackknife.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/distribution.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/special.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/alpha_diversity.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/period.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/ks.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/test.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/rarefaction.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats copying cogent/maths/stats/histogram.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/get_by_cai.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai copying cogent/maths/stats/cai/adaptor.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_unifrac.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/unifrac copying cogent/maths/unifrac/fast_tree.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/unifrac creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/spatial copying cogent/maths/spatial/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/spatial creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/motif copying cogent/motif/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/motif copying cogent/motif/k_word.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/motif copying cogent/motif/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/motif creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/gbseq.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/kegg_ko.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/dynalign.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/blast_xml.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/dialign.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/gcg.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/cigar.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/kegg_taxonomy.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/cut.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/comrna.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/hmmscan.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/clustal.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/illumina_sequence.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/locuslink.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/knetfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/blast.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/genbank.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/flowgram_parser.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/foldalign.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/cutg.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/ebi.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/ilm.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/contrafold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/binary_sff.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/infernal.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/ct.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/carnac.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/greengenes.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/fasta.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/bowtie.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/flowgram_collection.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/flowgram.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/dotur.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/kegg_fasta.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/bpseq.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/cove.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/column.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/gibbs.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/fastq.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/aaindex.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/gff.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/kegg_pos.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/consan.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/cmfinder.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/agilent_microarray.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/nupack.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/nexus.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/macsim.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/tree_xml.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/stockholm.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/newick.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/tree.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/tinyseq.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/table.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/pknotsrg.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/structure.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/ncbi_taxonomy.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/stride.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/msms.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rna_fold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/sprinzl.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rfam.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/sfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/record_finder.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/record.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/phylip.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/mothur.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rdb.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/psl.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/sequence.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/mfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/pdb.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/meme.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/unafold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/pfold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/paml_matrix.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/paml.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rnaview.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rnashapes.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rnaforester.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rnaalifold.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/unigene.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/rna_plot.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse copying cogent/parse/mage.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/tree_collection.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/least_squares.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/distance.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/nj.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/maximum_likelihood.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/consensus.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo copying cogent/phylo/tree_space.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation copying cogent/recalculation/definition.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation copying cogent/recalculation/calculation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation copying cogent/recalculation/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation copying cogent/recalculation/setting.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation copying cogent/recalculation/scope.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/searchpath.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/randomization.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/microarray_normalize.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/microarray.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/markov.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/birth_death.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/analysis.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/usage.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/tree.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim copying cogent/seqsim/sequence_generators.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/annotation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/selection.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/rna2d.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/pairs_util.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/manipulation.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/knots.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/dihedral.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/contact.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct copying cogent/struct/asa.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct creating build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/checkpointing.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/progress_display.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/array.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/__init__.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/terminal.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/unit_test.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/misc.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/option_parsing.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/warning.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/dict_array.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/table.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/parallel.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/modules.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/organizer.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/dict2d.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/transform.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/recode_alignment.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/trie.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/datatypes.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util copying cogent/util/update_version.py -> build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util running build_ext building 'cogent.align._compare' extension creating build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7 creating build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent creating build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/align/_compare.c -o build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_compare.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_compare.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_compare.so building 'cogent.align._pairwise_seqs' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/align/_pairwise_seqs.c -o build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_seqs.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_seqs.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_seqs.so building 'cogent.align._pairwise_pogs' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/align/_pairwise_pogs.c -o build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_pogs.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_pogs.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_pogs.so building 'cogent.evolve._solved_models' extension creating build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/evolve/_solved_models.c -o build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_solved_models.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_solved_models.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_solved_models.so building 'cogent.evolve._likelihood_tree' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/evolve/_likelihood_tree.c -o build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_likelihood_tree.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_likelihood_tree.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_likelihood_tree.so building 'cogent.evolve._pairwise_distance' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/evolve/_pairwise_distance.c -o build/temp.dragonfly-4.7-DEVELOPMENT-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:1777:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/evolve/_pairwise_distance.c:274: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_pairwise_distance.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_pairwise_distance.so building 'cogent.struct._asa' extension creating build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/struct/_asa.c -o build/temp.dragonfly-4.7-DEVELOPMENT-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:1777:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_asa.c:274: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/_asa.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/_asa.so building 'cogent.struct._contact' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/struct/_contact.c -o build/temp.dragonfly-4.7-DEVELOPMENT-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:1777:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_contact.c:274: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/_contact.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/_contact.so building 'cogent.maths._period' extension creating build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/maths/_period.c -o build/temp.dragonfly-4.7-DEVELOPMENT-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:1777:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/_period.c:274: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cogent/maths/_period.c: In function '__Pyx_c_abs_npy_float64': cogent/maths/_period.c:6845:20: warning: implicit declaration of function 'hypot_npy_float64' [-Wimplicit-function-declaration] return hypot_npy_float64(z.real, z.imag); ^ cogent/maths/_period.c: In function '__Pyx_c_pow_npy_float64': cogent/maths/_period.c:6884:25: warning: implicit declaration of function 'atan2_npy_float64' [-Wimplicit-function-declaration] theta = atan2_npy_float64(a.imag, a.real); ^ cogent/maths/_period.c:6886:19: warning: implicit declaration of function 'log_npy_float64' [-Wimplicit-function-declaration] lnr = log_npy_float64(r); ^ cogent/maths/_period.c:6887:19: warning: implicit declaration of function 'exp_npy_float64' [-Wimplicit-function-declaration] z_r = exp_npy_float64(lnr * b.real - theta * b.imag); ^ cogent/maths/_period.c:6889:28: warning: implicit declaration of function 'cos_npy_float64' [-Wimplicit-function-declaration] z.real = z_r * cos_npy_float64(z_theta); ^ cogent/maths/_period.c:6890:28: warning: implicit declaration of function 'sin_npy_float64' [-Wimplicit-function-declaration] z.imag = z_r * sin_npy_float64(z_theta); ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/_period.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/_period.so building 'cogent.maths.spatial.ckd3' extension creating build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/spatial cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c cogent/maths/spatial/ckd3.c -o build/temp.dragonfly-4.7-DEVELOPMENT-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:1777:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/spatial/ckd3.c:274: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/spatial/ckd3.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/spatial/ckd3.so =========================================================================== =================================================== ===> pycogent-1.9 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - found ===> pycogent-1.9 depends on file: /usr/local/bin/cython - found ===> pycogent-1.9 depends on file: /usr/local/bin/sphinx-build - found ===> pycogent-1.9 depends on package: py27-sqlalchemy10>=1.0.13 - found ===> pycogent-1.9 depends on package: py27-setuptools27>0 - found ===> pycogent-1.9 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =================================================== ===> Staging for pycogent-1.9 ===> Generating temporary packing list running install running build running build_py running build_ext running install_lib creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7 creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/distance_transform.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/solve.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/scipy_optimize.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/period.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/information_criteria.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai/adaptor.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai/get_by_cai.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/cai/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/histogram.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/alpha_diversity.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/distribution.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/special.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/kendall.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/jackknife.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/period.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/ks.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/test.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/stats/rarefaction.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/unifrac/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/unifrac/fast_tree.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/unifrac/fast_unifrac.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/geometry.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/svd.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/spatial/ckd3.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/spatial/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/fit_function.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix_exponentiation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix_exponential_integration.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/optimisers.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/scipy_optimisers.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/simannealingoptimiser.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix_logarithm.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/matrix/distance.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/function_optimisation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/markov.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/maths/_period.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/tree_collection.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/distance.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/maximum_likelihood.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/least_squares.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/nj.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/consensus.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/phylo/tree_space.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/rfam.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/feature_level.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/compara.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/host.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/database.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/region.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/sequence.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/assembly.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/species.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/genome.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/related_region.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ensembl/name.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/ncbi.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/pdb.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/db/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/fasta.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/kegg_taxonomy.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rnashapes.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rnaalifold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/structure.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/gbseq.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/meme.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/sprinzl.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/phylip.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/record_finder.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/unafold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/cutg.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/column.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/greengenes.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/foldalign.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/clustal.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/cove.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rna_fold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/cut.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rfam.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/ct.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/stockholm.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/nexus.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/pfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/psl.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/cigar.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/bpseq.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/binary_sff.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rnaforester.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/mothur.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/pknotsrg.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/kegg_pos.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/hmmscan.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/ilm.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/stride.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/dynalign.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/aaindex.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/sequence.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/illumina_sequence.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/paml_matrix.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/consan.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/ebi.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/cmfinder.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/record.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/gcg.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/blast_xml.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/tinyseq.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/gff.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/table.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/tree.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/tree_xml.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/fastq.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/genbank.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rnaview.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/kegg_ko.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/sfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/bowtie.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/dialign.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/macsim.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/msms.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/unigene.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/agilent_microarray.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/carnac.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/gibbs.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rdb.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/ncbi_taxonomy.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/flowgram_collection.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/flowgram_parser.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/comrna.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/rna_plot.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/contrafold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/pdb.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/knetfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/mage.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/nupack.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/mfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/newick.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/infernal.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/blast.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/dotur.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/flowgram.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/kegg_fasta.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/paml.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/parse/locuslink.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/distribution_plots.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/rlg2mpl.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/compatibility.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/linear.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/legend.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/dendrogram.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/dotplot.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/multivariate_plot.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/arrow_rates.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/dinuc.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/fancy_arrow.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/codon_usage.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/draw/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/infernal.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/carnac.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/rdp_classifier20.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/parameters.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/usearch.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/blast.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/dynalign.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/consan.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/rnashapes.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/dotur.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/fastq_join.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/contrafold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/formatdb.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/raxml_v730.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/blat.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/cove.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/dialign.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/cmfinder.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/flash.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/pandaseq.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/stride.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/fasttree.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/uclust.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/rdp_classifier.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/muscle.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/sfffile.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/cd_hit.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/unafold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/fasttree_v1.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/mfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/foldalign.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/sffinfo.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/sfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/mafft.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/seqprep.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/ilm.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/bwa.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/pplacer.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/rnaalifold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/pknotsrg.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/parsinsert.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/cdbfasta.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/rtax.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/mothur.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/rnaview.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/gctmpca.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/comrna.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/vienna_package.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/nupack.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/clustalw.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/raxml.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/guppy.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/knetfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/pfold.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/rnaforester.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/msms.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/muscle_v38.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/app/clearcut.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/coevolution.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/likelihood_tree.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/parameter_controller.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/simulate.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/models.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/likelihood_function.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/best_likelihood.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/motif_prob_model.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/solved_models.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/bootstrap.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/predicate.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/likelihood_calculation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/substitution_calculation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/discrete_markov.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/substitution_model.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/pairwise_distance.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_solved_models.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_likelihood_tree.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/evolve/_pairwise_distance.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/option_parsing.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/parallel.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/recode_alignment.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/datatypes.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/terminal.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/table.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/transform.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/unit_test.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/trie.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/array.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/dict2d.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/progress_display.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/modules.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/misc.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/checkpointing.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/warning.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/organizer.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/dict_array.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/update_version.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/util/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster/approximate_mds.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster/goodness_of_fit.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster/UPGMA.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster/nmds.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster/metric_scaling.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/cluster/procrustes.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/markov.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/birth_death.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/sequence_generators.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/randomization.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/microarray_normalize.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/tree.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/microarray.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/searchpath.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/analysis.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/seqsim/usage.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/entity.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/usage.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/bitvector.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/alignment.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/annotation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/tree.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/moltype.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/genetic_code.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/location.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/alphabet.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/profile.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/info.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/sequence.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/core/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/_asa.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/rna2d.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/dihedral.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/annotation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/manipulation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/selection.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/contact.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/knots.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/asa.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/pairs_util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/struct/_contact.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data/energy_params.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data/nucleic_properties.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data/protein_properties.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data/molecular_weight.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/data/ligand_properties.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation/scope.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation/calculation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation/setting.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/recalculation/definition.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/motif/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/motif/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/motif/k_word.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_pogs.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/dp_calculation.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/traceback.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/progressive.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/align.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/weights/methods.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/weights/util.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/weights/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/pycompare.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/indel_model.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/indel_positions.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/pairwise.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/algorithm.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_compare.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/align/_pairwise_seqs.so -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align creating /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/pdb_color.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/__init__.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/motif.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/structure.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/phylip.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/xyzrn.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/table.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/stockholm.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/rna_struct.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/alignment.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/fasta.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/text_tree.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/pdb.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/clustal.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/mage.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/bedgraph.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format copying build/lib.dragonfly-4.7-DEVELOPMENT-x86_64-2.7/cogent/format/nexus.py -> /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/distance_transform.py to distance_transform.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/solve.py to solve.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/scipy_optimize.py to scipy_optimize.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/period.py to period.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/information_criteria.py to information_criteria.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/adaptor.py to adaptor.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/get_by_cai.py to get_by_cai.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/cai/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/histogram.py to histogram.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/alpha_diversity.py to alpha_diversity.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/distribution.py to distribution.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/special.py to special.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/kendall.py to kendall.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/jackknife.py to jackknife.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/period.py to period.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/ks.py to ks.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/test.py to test.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/stats/rarefaction.py to rarefaction.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac/fast_tree.py to fast_tree.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/unifrac/fast_unifrac.py to fast_unifrac.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/geometry.py to geometry.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/svd.py to svd.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/spatial/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/fit_function.py to fit_function.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix_exponentiation.py to matrix_exponentiation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix_exponential_integration.py to matrix_exponential_integration.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/optimisers.py to optimisers.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/scipy_optimisers.py to scipy_optimisers.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/simannealingoptimiser.py to simannealingoptimiser.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix_logarithm.py to matrix_logarithm.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/matrix/distance.py to distance.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/function_optimisation.py to function_optimisation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/maths/markov.py to markov.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/tree_collection.py to tree_collection.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/distance.py to distance.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/maximum_likelihood.py to maximum_likelihood.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/least_squares.py to least_squares.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/nj.py to nj.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/consensus.py to consensus.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/phylo/tree_space.py to tree_space.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/rfam.py to rfam.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/feature_level.py to feature_level.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/compara.py to compara.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/host.py to host.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/database.py to database.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/region.py to region.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/sequence.py to sequence.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/assembly.py to assembly.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/species.py to species.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/genome.py to genome.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/related_region.py to related_region.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ensembl/name.py to name.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/ncbi.py to ncbi.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/pdb.py to pdb.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/db/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/fasta.py to fasta.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_taxonomy.py to kegg_taxonomy.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnashapes.py to rnashapes.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnaalifold.py to rnaalifold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/structure.py to structure.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gbseq.py to gbseq.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/meme.py to meme.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/sprinzl.py to sprinzl.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/phylip.py to phylip.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/record_finder.py to record_finder.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/unafold.py to unafold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cutg.py to cutg.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/column.py to column.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/greengenes.py to greengenes.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/foldalign.py to foldalign.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/clustal.py to clustal.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cove.py to cove.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rna_fold.py to rna_fold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cut.py to cut.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rfam.py to rfam.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ct.py to ct.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/stockholm.py to stockholm.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/nexus.py to nexus.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/pfold.py to pfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/psl.py to psl.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cigar.py to cigar.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/bpseq.py to bpseq.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/binary_sff.py to binary_sff.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnaforester.py to rnaforester.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/mothur.py to mothur.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/pknotsrg.py to pknotsrg.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_pos.py to kegg_pos.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/hmmscan.py to hmmscan.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ilm.py to ilm.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/stride.py to stride.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/dynalign.py to dynalign.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/aaindex.py to aaindex.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/sequence.py to sequence.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/illumina_sequence.py to illumina_sequence.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/paml_matrix.py to paml_matrix.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/consan.py to consan.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ebi.py to ebi.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/cmfinder.py to cmfinder.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/record.py to record.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gcg.py to gcg.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/blast_xml.py to blast_xml.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/tinyseq.py to tinyseq.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gff.py to gff.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/table.py to table.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/tree.py to tree.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/tree_xml.py to tree_xml.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/fastq.py to fastq.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/genbank.py to genbank.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rnaview.py to rnaview.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_ko.py to kegg_ko.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/sfold.py to sfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/bowtie.py to bowtie.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/dialign.py to dialign.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/macsim.py to macsim.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/msms.py to msms.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/unigene.py to unigene.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/agilent_microarray.py to agilent_microarray.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/carnac.py to carnac.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/gibbs.py to gibbs.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rdb.py to rdb.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/ncbi_taxonomy.py to ncbi_taxonomy.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/flowgram_collection.py to flowgram_collection.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/flowgram_parser.py to flowgram_parser.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/comrna.py to comrna.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/rna_plot.py to rna_plot.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/contrafold.py to contrafold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/pdb.py to pdb.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/knetfold.py to knetfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/mage.py to mage.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/nupack.py to nupack.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/mfold.py to mfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/newick.py to newick.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/infernal.py to infernal.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/blast.py to blast.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/dotur.py to dotur.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/flowgram.py to flowgram.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/kegg_fasta.py to kegg_fasta.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/paml.py to paml.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/parse/locuslink.py to locuslink.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/distribution_plots.py to distribution_plots.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/rlg2mpl.py to rlg2mpl.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/compatibility.py to compatibility.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/linear.py to linear.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/legend.py to legend.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/dendrogram.py to dendrogram.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/dotplot.py to dotplot.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/multivariate_plot.py to multivariate_plot.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/arrow_rates.py to arrow_rates.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/dinuc.py to dinuc.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/fancy_arrow.py to fancy_arrow.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/codon_usage.py to codon_usage.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/draw/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/infernal.py to infernal.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/carnac.py to carnac.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rdp_classifier20.py to rdp_classifier20.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/parameters.py to parameters.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/usearch.py to usearch.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/blast.py to blast.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/dynalign.py to dynalign.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/consan.py to consan.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnashapes.py to rnashapes.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/dotur.py to dotur.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/fastq_join.py to fastq_join.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/contrafold.py to contrafold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/formatdb.py to formatdb.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/raxml_v730.py to raxml_v730.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/blat.py to blat.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cove.py to cove.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/dialign.py to dialign.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cmfinder.py to cmfinder.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/flash.py to flash.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pandaseq.py to pandaseq.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/stride.py to stride.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/fasttree.py to fasttree.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/uclust.py to uclust.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rdp_classifier.py to rdp_classifier.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/muscle.py to muscle.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/sfffile.py to sfffile.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cd_hit.py to cd_hit.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/unafold.py to unafold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/fasttree_v1.py to fasttree_v1.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/mfold.py to mfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/foldalign.py to foldalign.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/sffinfo.py to sffinfo.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/sfold.py to sfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/mafft.py to mafft.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/seqprep.py to seqprep.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/ilm.py to ilm.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/bwa.py to bwa.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pplacer.py to pplacer.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnaalifold.py to rnaalifold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pknotsrg.py to pknotsrg.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/parsinsert.py to parsinsert.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/cdbfasta.py to cdbfasta.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rtax.py to rtax.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/mothur.py to mothur.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnaview.py to rnaview.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/gctmpca.py to gctmpca.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/comrna.py to comrna.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/vienna_package.py to vienna_package.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/nupack.py to nupack.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/clustalw.py to clustalw.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/raxml.py to raxml.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/guppy.py to guppy.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/knetfold.py to knetfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/pfold.py to pfold.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/rnaforester.py to rnaforester.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/msms.py to msms.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/muscle_v38.py to muscle_v38.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/app/clearcut.py to clearcut.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/coevolution.py to coevolution.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/likelihood_tree.py to likelihood_tree.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/parameter_controller.py to parameter_controller.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/simulate.py to simulate.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/models.py to models.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/likelihood_function.py to likelihood_function.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/best_likelihood.py to best_likelihood.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/motif_prob_model.py to motif_prob_model.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/solved_models.py to solved_models.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/bootstrap.py to bootstrap.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/predicate.py to predicate.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/likelihood_calculation.py to likelihood_calculation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/substitution_calculation.py to substitution_calculation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/discrete_markov.py to discrete_markov.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/substitution_model.py to substitution_model.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/evolve/pairwise_distance.py to pairwise_distance.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/option_parsing.py to option_parsing.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/parallel.py to parallel.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/recode_alignment.py to recode_alignment.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/datatypes.py to datatypes.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/terminal.py to terminal.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/table.py to table.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/transform.py to transform.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/unit_test.py to unit_test.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/trie.py to trie.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/array.py to array.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/dict2d.py to dict2d.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/progress_display.py to progress_display.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/modules.py to modules.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/misc.py to misc.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/checkpointing.py to checkpointing.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/warning.py to warning.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/organizer.py to organizer.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/dict_array.py to dict_array.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/update_version.py to update_version.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/util/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/approximate_mds.py to approximate_mds.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/goodness_of_fit.py to goodness_of_fit.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/UPGMA.py to UPGMA.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/nmds.py to nmds.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/metric_scaling.py to metric_scaling.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/cluster/procrustes.py to procrustes.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/markov.py to markov.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/birth_death.py to birth_death.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/sequence_generators.py to sequence_generators.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/randomization.py to randomization.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/microarray_normalize.py to microarray_normalize.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/tree.py to tree.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/microarray.py to microarray.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/searchpath.py to searchpath.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/analysis.py to analysis.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/seqsim/usage.py to usage.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/entity.py to entity.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/usage.py to usage.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/bitvector.py to bitvector.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/alignment.py to alignment.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/annotation.py to annotation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/tree.py to tree.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/moltype.py to moltype.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/genetic_code.py to genetic_code.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/location.py to location.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/alphabet.py to alphabet.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/profile.py to profile.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/info.py to info.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/sequence.py to sequence.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/core/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/rna2d.py to rna2d.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/dihedral.py to dihedral.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/annotation.py to annotation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/manipulation.py to manipulation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/selection.py to selection.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/contact.py to contact.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/knots.py to knots.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/asa.py to asa.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/struct/pairs_util.py to pairs_util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/energy_params.py to energy_params.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/nucleic_properties.py to nucleic_properties.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/protein_properties.py to protein_properties.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/molecular_weight.py to molecular_weight.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/data/ligand_properties.py to ligand_properties.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/scope.py to scope.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/calculation.py to calculation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/setting.py to setting.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/recalculation/definition.py to definition.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/motif/k_word.py to k_word.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/dp_calculation.py to dp_calculation.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/traceback.py to traceback.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/progressive.py to progressive.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/align.py to align.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights/methods.py to methods.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights/util.py to util.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/weights/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/pycompare.py to pycompare.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/indel_model.py to indel_model.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/indel_positions.py to indel_positions.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/pairwise.py to pairwise.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/align/algorithm.py to algorithm.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/pdb_color.py to pdb_color.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/__init__.py to __init__.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/motif.py to motif.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/structure.py to structure.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/phylip.py to phylip.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/xyzrn.py to xyzrn.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/table.py to table.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/stockholm.py to stockholm.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/rna_struct.py to rna_struct.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/alignment.py to alignment.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/fasta.py to fasta.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/text_tree.py to text_tree.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/pdb.py to pdb.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/clustal.py to clustal.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/mage.py to mage.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/bedgraph.py to bedgraph.pyc byte-compiling /wrkdirs/biology/pycogent/stage/usr/local/lib/python2.7/site-packages/cogent/format/nexus.py to nexus.pyc writing byte-compilation script '/tmp/tmpidZMHX.py' /usr/local/bin/python2.7 -O /tmp/tmpidZMHX.py removing /tmp/tmpidZMHX.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 /wrkdirs/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 '/wrkdirs/biology/pycogent/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for pycogent-1.9 file sizes/checksums [1065]: .......... done packing files [1065]: .......... done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for pycogent-1.9 build of biology/pycogent ended at Tue Oct 4 22:02:06 PDT 2016 build time: 00:02:20