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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