Friday, February 22, 2013

install biopython on osX 10.8.2 Mountain Lion

Goal: Install current biopython on laptop "Byte" with os 10.8.2.

 $ which make
/usr/bin/make
$ port search biopython
py-biopython @1.61 (python, science)
    python tools for computational molecular biology

py25-biopython @1.61 (python, science)
    python tools for computational molecular biology

py26-biopython @1.61 (python, science)
    python tools for computational molecular biology

py27-biopython @1.61 (python, science)
    python tools for computational molecular biology

Found 4 ports.
$ sudo port install py27-biopython @1.61
Password:

Password:
--->  Computing dependencies for py27-biopython
--->  Dependencies to be installed: flex gettext expat libiconv ncurses m4 py27-numpy fftw-3 py27-nose nosetests_select py27-distribute python27 bzip2 db46 libedit openssl zlib python_select sqlite3 py27-reportlab py27-pil freetype lcms jpeg tiff xz py27-tkinter tk tcl xorg-libX11 xorg-kbproto xorg-libXau xorg-xproto xorg-libXdmcp xorg-libxcb xorg-libpthread-stubs xorg-xcb-proto libxml2
--->  Fetching archive for expat
--->  Attempting to fetch expat-2.1.0_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/expat
--->  Attempting to fetch expat-2.1.0_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/expat
--->  Installing expat @2.1.0_0
--->  Activating expat @2.1.0_0
--->  Cleaning expat
--->  Fetching archive for libiconv
--->  Attempting to fetch libiconv-1.14_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/libiconv
--->  Attempting to fetch libiconv-1.14_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/libiconv
--->  Installing libiconv @1.14_0
--->  Activating libiconv @1.14_0
--->  Cleaning libiconv
--->  Fetching archive for ncurses
--->  Attempting to fetch ncurses-5.9_2.darwin_12.x86_64.tbz2 from http://packages.macports.org/ncurses
--->  Attempting to fetch ncurses-5.9_2.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/ncurses
--->  Installing ncurses @5.9_2
--->  Activating ncurses @5.9_2
--->  Cleaning ncurses
--->  Fetching archive for gettext
--->  Attempting to fetch gettext-0.18.2_2.darwin_12.x86_64.tbz2 from http://packages.macports.org/gettext
--->  Attempting to fetch gettext-0.18.2_2.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/gettext
--->  Installing gettext @0.18.2_2
--->  Activating gettext @0.18.2_2
--->  Cleaning gettext
--->  Fetching archive for m4
--->  Attempting to fetch m4-1.4.16_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/m4
--->  Attempting to fetch m4-1.4.16_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/m4
--->  Installing m4 @1.4.16_0
--->  Activating m4 @1.4.16_0
--->  Cleaning m4
--->  Fetching archive for flex
--->  Attempting to fetch flex-2.5.37_1.darwin_12.x86_64.tbz2 from http://packages.macports.org/flex
--->  Attempting to fetch flex-2.5.37_1.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/flex
--->  Installing flex @2.5.37_1
--->  Activating flex @2.5.37_1
--->  Cleaning flex
--->  Fetching archive for fftw-3
--->  Attempting to fetch fftw-3-3.3.3_1.darwin_12.x86_64.tbz2 from http://packages.macports.org/fftw-3
--->  Attempting to fetch fftw-3-3.3.3_1.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/fftw-3
--->  Installing fftw-3 @3.3.3_1
--->  Activating fftw-3 @3.3.3_1
--->  Cleaning fftw-3
--->  Fetching archive for nosetests_select
--->  Attempting to fetch nosetests_select-0.1_0.darwin_12.noarch.tbz2 from http://packages.macports.org/nosetests_select
--->  Attempting to fetch nosetests_select-0.1_0.darwin_12.noarch.tbz2.rmd160 from http://packages.macports.org/nosetests_select
--->  Installing nosetests_select @0.1_0
--->  Activating nosetests_select @0.1_0
--->  Cleaning nosetests_select
--->  Fetching archive for bzip2
--->  Attempting to fetch bzip2-1.0.6_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/bzip2
--->  Attempting to fetch bzip2-1.0.6_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/bzip2
--->  Installing bzip2 @1.0.6_0
--->  Activating bzip2 @1.0.6_0
--->  Cleaning bzip2
--->  Fetching archive for db46
--->  Attempting to fetch db46-4.6.21_7.darwin_12.x86_64.tbz2 from http://packages.macports.org/db46
--->  Attempting to fetch db46-4.6.21_7.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/db46
--->  Installing db46 @4.6.21_7
--->  Activating db46 @4.6.21_7
^[[A--->  Cleaning db46
--->  Fetching archive for libedit
--->  Attempting to fetch libedit-20121213-3.0_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/libedit
--->  Attempting to fetch libedit-20121213-3.0_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/libedit
--->  Installing libedit @20121213-3.0_0
--->  Activating libedit @20121213-3.0_0
--->  Cleaning libedit
--->  Fetching archive for zlib
--->  Attempting to fetch zlib-1.2.7_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/zlib
--->  Attempting to fetch zlib-1.2.7_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/zlib
--->  Installing zlib @1.2.7_0
--->  Activating zlib @1.2.7_0
--->  Cleaning zlib
--->  Fetching archive for openssl
--->  Attempting to fetch openssl-1.0.1e_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/openssl
--->  Attempting to fetch openssl-1.0.1e_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/openssl
--->  Installing openssl @1.0.1e_0
--->  Activating openssl @1.0.1e_0
--->  Cleaning openssl
--->  Fetching archive for python_select
--->  Attempting to fetch python_select-0.3_2.darwin_12.noarch.tbz2 from http://packages.macports.org/python_select
--->  Attempting to fetch python_select-0.3_2.darwin_12.noarch.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/python_select
--->  Attempting to fetch python_select-0.3_2.darwin_12.noarch.tbz2 from http://lil.fr.packages.macports.org/python_select
--->  Attempting to fetch python_select-0.3_2.darwin_12.noarch.tbz2 from http://jog.id.packages.macports.org/macports/packages/python_select
--->  Fetching distfiles for python_select
--->  Verifying checksum(s) for python_select
--->  Extracting python_select
--->  Configuring python_select
--->  Building python_select
--->  Staging python_select into destroot
--->  Installing python_select @0.3_2
--->  Activating python_select @0.3_2
--->  Cleaning python_select
--->  Fetching archive for sqlite3
--->  Attempting to fetch sqlite3-3.7.15.2_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/sqlite3
--->  Attempting to fetch sqlite3-3.7.15.2_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/sqlite3
--->  Installing sqlite3 @3.7.15.2_0
--->  Activating sqlite3 @3.7.15.2_0
--->  Cleaning sqlite3
--->  Fetching archive for python27
--->  Attempting to fetch python27-2.7.3_1.darwin_12.x86_64.tbz2 from http://packages.macports.org/python27
--->  Attempting to fetch python27-2.7.3_1.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/python27
--->  Installing python27 @2.7.3_1
--->  Activating python27 @2.7.3_1

To make python 2.7 the default (i.e. the version you get when you run 'python'), please run:

sudo port select --set python python27

--->  Cleaning python27
--->  Fetching archive for py27-distribute
--->  Attempting to fetch py27-distribute-0.6.35_0.darwin_12.noarch.tbz2 from http://packages.macports.org/py27-distribute
--->  Attempting to fetch py27-distribute-0.6.35_0.darwin_12.noarch.tbz2.rmd160 from http://packages.macports.org/py27-distribute
--->  Installing py27-distribute @0.6.35_0
--->  Activating py27-distribute @0.6.35_0
--->  Cleaning py27-distribute
--->  Fetching archive for py27-nose
--->  Attempting to fetch py27-nose-1.2.1_1.darwin_12.noarch.tbz2 from http://packages.macports.org/py27-nose
--->  Attempting to fetch py27-nose-1.2.1_1.darwin_12.noarch.tbz2.rmd160 from http://packages.macports.org/py27-nose
--->  Installing py27-nose @1.2.1_1
--->  Activating py27-nose @1.2.1_1
--->  Cleaning py27-nose
--->  Fetching archive for py27-numpy
--->  Attempting to fetch py27-numpy-1.6.2_1.darwin_12.x86_64.tbz2 from http://packages.macports.org/py27-numpy
^[[B--->  Attempting to fetch py27-numpy-1.6.2_1.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/py27-numpy
--->  Installing py27-numpy @1.6.2_1
--->  Activating py27-numpy @1.6.2_1
--->  Cleaning py27-numpy
--->  Fetching archive for freetype
--->  Attempting to fetch freetype-2.4.10_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/freetype
--->  Attempting to fetch freetype-2.4.10_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/freetype
--->  Installing freetype @2.4.10_0
--->  Activating freetype @2.4.10_0
--->  Cleaning freetype
--->  Fetching archive for jpeg
--->  Attempting to fetch jpeg-9_1.darwin_12.x86_64.tbz2 from http://packages.macports.org/jpeg
--->  Attempting to fetch jpeg-9_1.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/jpeg
--->  Installing jpeg @9_1
--->  Activating jpeg @9_1
--->  Cleaning jpeg
--->  Fetching archive for xz
--->  Attempting to fetch xz-5.0.4_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/xz
--->  Attempting to fetch xz-5.0.4_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/xz
--->  Installing xz @5.0.4_0
--->  Activating xz @5.0.4_0
--->  Cleaning xz
--->  Fetching archive for tiff
--->  Attempting to fetch tiff-4.0.3_1.darwin_12.x86_64.tbz2 from http://packages.macports.org/tiff
--->  Attempting to fetch tiff-4.0.3_1.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/tiff
--->  Installing tiff @4.0.3_1
--->  Activating tiff @4.0.3_1
--->  Cleaning tiff
--->  Fetching archive for lcms
--->  Attempting to fetch lcms-1.19_5.darwin_12.x86_64.tbz2 from http://packages.macports.org/lcms
--->  Attempting to fetch lcms-1.19_5.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/lcms
--->  Installing lcms @1.19_5
--->  Activating lcms @1.19_5
--->  Cleaning lcms
--->  Fetching archive for tcl
--->  Attempting to fetch tcl-8.6.0_1+corefoundation+threads.darwin_12.x86_64.tbz2 from http://packages.macports.org/tcl
--->  Attempting to fetch tcl-8.6.0_1+corefoundation+threads.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/tcl
--->  Installing tcl @8.6.0_1+corefoundation+threads
--->  Activating tcl @8.6.0_1+corefoundation+threads
--->  Cleaning tcl
--->  Fetching archive for xorg-kbproto
--->  Attempting to fetch xorg-kbproto-1.0.6_0.darwin_12.noarch.tbz2 from http://packages.macports.org/xorg-kbproto
--->  Attempting to fetch xorg-kbproto-1.0.6_0.darwin_12.noarch.tbz2.rmd160 from http://packages.macports.org/xorg-kbproto
--->  Installing xorg-kbproto @1.0.6_0
--->  Activating xorg-kbproto @1.0.6_0
--->  Cleaning xorg-kbproto
--->  Fetching archive for xorg-xproto
--->  Attempting to fetch xorg-xproto-7.0.23_0.darwin_12.noarch.tbz2 from http://packages.macports.org/xorg-xproto
--->  Attempting to fetch xorg-xproto-7.0.23_0.darwin_12.noarch.tbz2.rmd160 from http://packages.macports.org/xorg-xproto
--->  Installing xorg-xproto @7.0.23_0
--->  Activating xorg-xproto @7.0.23_0
--->  Cleaning xorg-xproto
--->  Fetching archive for xorg-libXau
--->  Attempting to fetch xorg-libXau-1.0.7_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/xorg-libXau
--->  Attempting to fetch xorg-libXau-1.0.7_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/xorg-libXau
--->  Installing xorg-libXau @1.0.7_0
--->  Activating xorg-libXau @1.0.7_0
--->  Cleaning xorg-libXau
--->  Fetching archive for xorg-libXdmcp
--->  Attempting to fetch xorg-libXdmcp-1.1.1_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/xorg-libXdmcp
--->  Attempting to fetch xorg-libXdmcp-1.1.1_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/xorg-libXdmcp
--->  Installing xorg-libXdmcp @1.1.1_0
--->  Activating xorg-libXdmcp @1.1.1_0
--->  Cleaning xorg-libXdmcp
--->  Fetching archive for xorg-libpthread-stubs
--->  Attempting to fetch xorg-libpthread-stubs-0.3_0.darwin_12.noarch.tbz2 from http://packages.macports.org/xorg-libpthread-stubs
--->  Attempting to fetch xorg-libpthread-stubs-0.3_0.darwin_12.noarch.tbz2.rmd160 from http://packages.macports.org/xorg-libpthread-stubs
--->  Installing xorg-libpthread-stubs @0.3_0
--->  Activating xorg-libpthread-stubs @0.3_0
--->  Cleaning xorg-libpthread-stubs
--->  Fetching archive for libxml2
--->  Attempting to fetch libxml2-2.8.0_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/libxml2
--->  Attempting to fetch libxml2-2.8.0_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/libxml2
--->  Installing libxml2 @2.8.0_0
--->  Activating libxml2 @2.8.0_0
--->  Cleaning libxml2
--->  Fetching archive for xorg-xcb-proto
--->  Attempting to fetch xorg-xcb-proto-1.8_0+python27.darwin_12.noarch.tbz2 from http://packages.macports.org/xorg-xcb-proto
--->  Attempting to fetch xorg-xcb-proto-1.8_0+python27.darwin_12.noarch.tbz2.rmd160 from http://packages.macports.org/xorg-xcb-proto
--->  Installing xorg-xcb-proto @1.8_0+python27
--->  Activating xorg-xcb-proto @1.8_0+python27
--->  Cleaning xorg-xcb-proto
--->  Fetching archive for xorg-libxcb
--->  Attempting to fetch xorg-libxcb-1.9_0+python27.darwin_12.x86_64.tbz2 from http://packages.macports.org/xorg-libxcb
--->  Attempting to fetch xorg-libxcb-1.9_0+python27.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/xorg-libxcb
--->  Installing xorg-libxcb @1.9_0+python27
--->  Activating xorg-libxcb @1.9_0+python27
--->  Cleaning xorg-libxcb
--->  Fetching archive for xorg-libX11
--->  Attempting to fetch xorg-libX11-1.5.0_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/xorg-libX11
--->  Attempting to fetch xorg-libX11-1.5.0_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/xorg-libX11
--->  Installing xorg-libX11 @1.5.0_0
--->  Activating xorg-libX11 @1.5.0_0
--->  Cleaning xorg-libX11
--->  Fetching archive for tk
--->  Attempting to fetch tk-8.6.0_1+quartz.darwin_12.x86_64.tbz2 from http://packages.macports.org/tk
--->  Attempting to fetch tk-8.6.0_1+quartz.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/tk
--->  Installing tk @8.6.0_1+quartz
--->  Activating tk @8.6.0_1+quartz
--->  Cleaning tk
--->  Fetching archive for py27-tkinter
--->  Attempting to fetch py27-tkinter-2.7.3_2.darwin_12.x86_64.tbz2 from http://packages.macports.org/py27-tkinter
--->  Attempting to fetch py27-tkinter-2.7.3_2.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/py27-tkinter
--->  Installing py27-tkinter @2.7.3_2
--->  Activating py27-tkinter @2.7.3_2
--->  Cleaning py27-tkinter
--->  Fetching archive for py27-pil
--->  Attempting to fetch py27-pil-1.1.7_6.darwin_12.x86_64.tbz2 from http://packages.macports.org/py27-pil
--->  Attempting to fetch py27-pil-1.1.7_6.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/py27-pil
--->  Installing py27-pil @1.1.7_6
--->  Activating py27-pil @1.1.7_6
--->  Cleaning py27-pil
--->  Fetching archive for py27-reportlab
--->  Attempting to fetch py27-reportlab-2.6_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/py27-reportlab
--->  Attempting to fetch py27-reportlab-2.6_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/py27-reportlab
--->  Installing py27-reportlab @2.6_0
--->  Activating py27-reportlab @2.6_0
--->  Cleaning py27-reportlab
--->  Fetching archive for py27-biopython
--->  Attempting to fetch py27-biopython-1.61_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/py27-biopython
--->  Attempting to fetch py27-biopython-1.61_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/py27-biopython
--->  Installing py27-biopython @1.61_0
--->  Activating py27-biopython @1.61_0
--->  Cleaning py27-biopython
--->  Updating database of binaries: 100.0%
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.



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