Macports py26-numpy Issue on OS X Mavericks

david laxer dbl001 at yahoo.com
Fri Nov 22 13:38:42 PST 2013


I did this:

  701  sudo port -v selfupdate
  703  sudo  port upgrade outdated

Also, this:

  733  port -qv installed > myports.txt
  734  sudo port -f uninstall installed
  735  sudo port clean all

and this:

sudo ./restore_ports.tcl myports.txt

>> Why does 
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/_methods.py already exist if it does not belong to a port?

I've done Ruby work in the past.  Also, Boost installation.   Could Brew cause this?




On Friday, November 22, 2013 1:30 PM, Ryan Schmidt <ryandesign at macports.org> wrote:
 
Remember to Reply All so this discussion remains on the mailing list and does not move to private email.



On Nov 22, 2013, at 15:26, david laxer wrote:

> Hi Ryan,
> 
> I tried this:
> 
> David-Laxers-MacBook-Pro:~ davidlaxer$ sudo port clean py26-numpy
> Password:
> --->  Cleaning py26-numpy
> David-Laxers-MacBook-Pro:~ davidlaxer$ sudo port clean python26
> --->  Cleaning python26
> David-Laxers-MacBook-Pro:~ davidlaxer$ 
> 
> Next, 
> 
> David-Laxers-MacBook-Pro:~ davidlaxer$ sudo ./restore_ports.tcl myports.txt
> Warning: Skipping ncursesw (not in the ports tree)
> --->  Cleaning bzip2
> --->  Cleaning cctools-headers
> --->  Cleaning db_select
> --->  Cleaning expat
> --->  Cleaning expat
> --->  Cleaning fftw-3
> --->  Cleaning fftw-3
> --->  Cleaning gcc_select
> --->  Cleaning gmp
> --->  Cleaning gmp
> --->  Cleaning gperf
> --->  Cleaning gperf
> --->  Cleaning icu
> --->  Cleaning icu
> --->  Cleaning libffi
> --->  Cleaning libiconv
> --->  Cleaning libiconv
> --->  Cleaning llvm_select
> --->  Cleaning m4
> --->  Cleaning ncurses
> --->  Cleaning ncurses
> --->  Cleaning ncurses
> --->  Cleaning nosetests_select
> --->  Cleaning nspr
> --->  Cleaning nspr
> --->  Computing dependencies for pkgconfig
> --->  Cleaning pkgconfig
> --->  Computing dependencies for pkgconfig
> --->  Cleaning pkgconfig
> --->  Configuring py26-distribute
> Error: py26-distribute is obsolete, please install py26-setuptools instead.
> Error: org.macports.configure for port py26-distribute returned: obsolete port
> Please see the log file for port py26-distribute for details:
>     /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-distribute/py26-distribute/main.log

> --->  Cleaning python_select
> --->  Cleaning python_select
> --->  Computing dependencies for readline
> --->  Cleaning readline
> --->  Computing dependencies for readline
> --->  Cleaning readline
> --->  Computing dependencies for spidermonkey
> --->  Cleaning spidermonkey
> --->  Computing dependencies for spidermonkey185
> --->  Cleaning spidermonkey185
> --->  Cleaning tcl
> --->  Cleaning tcl
> --->  Cleaning tcp_wrappers
> --->  Cleaning xorg-bigreqsproto
> --->  Cleaning xorg-bigreqsproto
> --->  Cleaning xorg-inputproto
> --->  Cleaning xorg-inputproto
> --->  Cleaning xorg-kbproto
> --->  Cleaning xorg-kbproto
> --->  Cleaning xorg-libpthread-stubs
> --->  Cleaning xorg-renderproto
> --->  Cleaning xorg-scrnsaverproto
> --->  Cleaning xorg-util-macros
> --->  Cleaning xorg-util-macros
> --->  Cleaning xorg-xcmiscproto
> --->  Cleaning xorg-xcmiscproto
> --->  Cleaning xorg-xextproto
> --->  Cleaning xorg-xextproto
> --->  Cleaning xorg-xf86bigfontproto
> --->  Cleaning xorg-xproto
> --->  Cleaning xorg-xproto
> --->  Cleaning xorg-xtrans
> --->  Cleaning xorg-xtrans
> --->  Computing dependencies for dbus
> --->  Cleaning dbus
> --->  Computing dependencies for dbus
> --->  Cleaning dbus
> --->  Computing dependencies for gettext
> --->  Cleaning gettext
> --->  Computing dependencies for gettext
> --->  Cleaning gettext
> --->  Computing dependencies for libedit
> --->  Cleaning libedit
> --->  Computing dependencies for libidn
> --->  Cleaning libidn
> --->  Computing dependencies for libidn
> --->  Cleaning libidn
> --->  Computing dependencies for sqlite3
> --->  Cleaning sqlite3
> --->  Computing dependencies for sqlite3
> --->  Cleaning sqlite3
> --->  Computing dependencies for xorg-libXau
> --->  Cleaning xorg-libXau
> --->  Computing dependencies for xorg-libXau
> --->  Cleaning xorg-libXau
> --->  Cleaning xorg-libXdmcp
> --->  Cleaning xorg-libXdmcp
> --->  Computing dependencies for xz
> --->  Cleaning xz
> --->  Computing dependencies for xz
> --->  Cleaning xz
> --->  Computing dependencies for yasm
> --->  Cleaning yasm
> --->  Cleaning zlib
> --->  Cleaning zlib
> --->  Computing dependencies for gawk
> --->  Cleaning gawk
> --->  Computing dependencies for gawk
> --->  Cleaning gawk
> --->  Computing dependencies for gdbm
> --->  Cleaning gdbm
> --->  Computing dependencies for gdbm
> --->  Cleaning gdbm
> --->  Computing dependencies for glpk
> --->  Cleaning glpk
> --->  Computing dependencies for libpng
> --->  Cleaning libpng
> --->  Computing dependencies for libpng
> --->  Cleaning libpng
> --->  Computing dependencies for libxml2
> --->  Cleaning libxml2
> --->  Computing dependencies for libxml2
> --->  Cleaning libxml2
> --->  Computing dependencies for mpfr
> --->  Cleaning mpfr
> --->  Computing dependencies for mpfr
> --->  Cleaning mpfr
> --->  Computing dependencies for openssl
> --->  Cleaning openssl
> --->  Computing dependencies for openssl
> --->  Cleaning openssl
> --->  Computing dependencies for openssl
> --->  Cleaning openssl
> --->  Computing dependencies for perl5.12
> --->  Cleaning perl5.12
> --->  Computing dependencies for perl5.12
> --->  Cleaning perl5.12
> --->  Computing dependencies for ppl
> --->  Cleaning ppl
> --->  Computing dependencies for texinfo
> --->  Cleaning texinfo
> --->  Computing dependencies for freetype
> --->  Cleaning freetype
> --->  Computing dependencies for freetype
> --->  Cleaning freetype
> --->  Cleaning gzip
> --->  Cleaning gzip
> --->  Computing dependencies for libmpc
> --->  Cleaning libmpc
> --->  Computing dependencies for p5.12-locale-gettext
> --->  Cleaning p5.12-locale-gettext
> --->  Computing dependencies for perl5
> --->  Cleaning perl5
> --->  Computing dependencies for perl5
> --->  Cleaning perl5
> --->  Computing dependencies for autoconf
> --->  Cleaning autoconf
> --->  Computing dependencies for autoconf
> --->  Cleaning autoconf
> --->  Computing dependencies for autoconf213
> --->  Cleaning autoconf213
> --->  Computing dependencies for automake
> --->  Cleaning automake
> --->  Computing dependencies for automake
> --->  Cleaning automake
> --->  Cleaning curl-ca-bundle
> --->  Cleaning curl-ca-bundle
> --->  Cleaning curl-ca-bundle
> --->  Computing dependencies for erlang
> --->  Cleaning erlang
> --->  Computing dependencies for erlang
> --->  Cleaning erlang
> --->  Computing dependencies for fontconfig
> --->  Cleaning fontconfig
> --->  Computing dependencies for fontconfig
> --->  Cleaning fontconfig
> --->  Computing dependencies for glib2
> --->  Cleaning glib2
> --->  Computing dependencies for glib2
> --->  Cleaning glib2
> --->  Computing dependencies for help2man
> --->  Cleaning help2man
> --->  Computing dependencies for help2man
> --->  Cleaning help2man
> --->  Computing dependencies for libidl
> --->  Cleaning libidl
> --->  Computing dependencies for libidl
> --->  Cleaning libidl
> --->  Cleaning libtool
> --->  Cleaning libtool
> --->  Computing dependencies for llvm-3.3
> --->  Cleaning llvm-3.3
> --->  Computing dependencies for p5-locale-gettext
> --->  Cleaning p5-locale-gettext
> --->  Computing dependencies for curl
> --->  Cleaning curl
> --->  Computing dependencies for curl
> --->  Cleaning curl
> --->  Computing dependencies for curl
> --->  Cleaning curl
> --->  Computing dependencies for db46
> --->  Cleaning db46
> --->  Computing dependencies for db46
> --->  Cleaning db46
> --->  Computing dependencies for isl
> --->  Cleaning isl
> --->  Computing dependencies for ld64
> --->  Cleaning ld64
> --->  Computing dependencies for python26
> --->  Cleaning python26
> --->  Computing dependencies for python26
> --->  Cleaning python26
> --->  Computing dependencies for python27
> --->  Cleaning python27
> --->  Computing dependencies for python27
> --->  Cleaning python27
> --->  Computing dependencies for xorg-xcb-proto
> --->  Cleaning xorg-xcb-proto
> --->  Computing dependencies for xorg-xcb-proto
> --->  Cleaning xorg-xcb-proto
> --->  Computing dependencies for boost
> --->  Cleaning boost
> --->  Computing dependencies for cctools
> --->  Cleaning cctools
> --->  Computing dependencies for cloog
> --->  Cleaning cloog
> --->  Computing dependencies for couchdb
> --->  Cleaning couchdb
> --->  Computing dependencies for couchdb
> --->  Cleaning couchdb
> --->  Computing dependencies for libgcc
> --->  Cleaning libgcc
> --->  Computing dependencies for libgcc45
> --->  Cleaning libgcc45
> --->  Computing dependencies for llvm-gcc42
> --->  Cleaning llvm-gcc42
> --->  Computing dependencies for mysql5
> --->  Cleaning mysql5
> --->  Computing dependencies for mysql5
> --->  Cleaning mysql5
> --->  Computing dependencies for mysql5
> --->  Cleaning mysql5
> --->  Computing dependencies for mysql5-server
> --->  Cleaning mysql5-server
> --->  Computing dependencies for mysql5-server
> --->  Cleaning mysql5-server
> --->  Computing dependencies for mysql5-server
> --->  Cleaning mysql5-server
> --->  Computing dependencies for py26-configobj
> --->  Cleaning py26-configobj
> --->  Computing dependencies for py26-configobj
> --->  Cleaning py26-configobj
> --->  Computing dependencies for py26-parsing
> --->  Cleaning py26-parsing
> --->  Computing dependencies for py26-setuptools
> --->  Cleaning py26-setuptools
> --->  Computing dependencies for py26-six
> --->  Cleaning py26-six
> --->  Computing dependencies for py26-tornado
> --->  Cleaning py26-tornado
> --->  Computing dependencies for py26-tz
> --->  Cleaning py26-tz
> --->  Computing dependencies for py26-tz
> --->  Cleaning py26-tz
> --->  Computing dependencies for py27-setuptools
> --->  Cleaning py27-setuptools
> --->  Computing dependencies for xorg-libxcb
> --->  Cleaning xorg-libxcb
> --->  Computing dependencies for xorg-libxcb
> --->  Cleaning xorg-libxcb
> --->  Computing dependencies for gcc44
> --->  Cleaning gcc44
> --->  Computing dependencies for gcc44
> --->  Cleaning gcc44
> --->  Computing dependencies for gcc47
> --->  Cleaning gcc47
> --->  Computing dependencies for py26-altgraph
> --->  Cleaning py26-altgraph
> --->  Computing dependencies for py26-altgraph
> --->  Cleaning py26-altgraph
> --->  Computing dependencies for py26-bdist_mpkg
> --->  Cleaning py26-bdist_mpkg
> --->  Computing dependencies for py26-bdist_mpkg
> --->  Cleaning py26-bdist_mpkg
> --->  Computing dependencies for py26-dateutil
> --->  Cleaning py26-dateutil
> --->  Computing dependencies for py26-dateutil
> --->  Cleaning py26-dateutil
> --->  Computing dependencies for py26-modulegraph
> --->  Cleaning py26-modulegraph
> --->  Computing dependencies for py26-modulegraph
> --->  Cleaning py26-modulegraph
> --->  Computing dependencies for py26-nose
> --->  Cleaning py26-nose
> --->  Computing dependencies for py26-nose
> --->  Cleaning py26-nose
> --->  Computing dependencies for py27-roman
> --->  Cleaning py27-roman
> --->  Computing dependencies for xorg-libX11
> --->  Cleaning xorg-libX11
> --->  Computing dependencies for xorg-libX11
> --->  Cleaning xorg-libX11
> --->  Computing dependencies for xorg-libXext
> --->  Cleaning xorg-libXext
> --->  Computing dependencies for xorg-libXScrnSaver
> --->  Cleaning xorg-libXScrnSaver
> --->  Computing dependencies for xrender
> --->  Cleaning xrender
> --->  Computing dependencies for atlas
> --->  Cleaning atlas
> --->  Computing dependencies for atlas
> --->  Cleaning atlas
> --->  Computing dependencies for py26-macholib
> --->  Cleaning py26-macholib
> --->  Computing dependencies for py26-macholib
> --->  Cleaning py26-macholib
> --->  Computing dependencies for py26-py2app
> --->  Cleaning py26-py2app
> --->  Computing dependencies for py26-py2app
> --->  Cleaning py26-py2app
> --->  Computing dependencies for py26-pyobjc
> --->  Cleaning py26-pyobjc
> --->  Computing dependencies for py26-pyobjc
> --->  Cleaning py26-pyobjc
> --->  Computing dependencies for py26-pyobjc-cocoa
> --->  Cleaning py26-pyobjc-cocoa
> --->  Computing dependencies for py26-pyobjc-cocoa
> --->  Cleaning py26-pyobjc-cocoa
> --->  Computing dependencies for py27-docutils
> --->  Cleaning py27-docutils
> --->  Computing dependencies for tk
> --->  Cleaning tk
> --->  Computing dependencies for tk
> --->  Cleaning tk
> --->  Computing dependencies for Xft2
> --->  Cleaning Xft2
> --->  Computing dependencies for mercurial
> --->  Cleaning mercurial
> --->  Computing dependencies for mercurial
> --->  Cleaning mercurial
> --->  Computing dependencies for py26-tkinter
> --->  Cleaning py26-tkinter
> --->  Computing dependencies for py26-tkinter
> --->  Cleaning py26-tkinter
> --->  Computing dependencies for py26-matplotlib
> --->  Dependencies to be installed: py26-numpy
> --->  Activating py26-numpy @1.8.0_0
> Error: org.macports.activate for port py26-numpy returned: Image error: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/_methods.py already exists and does not belong to a registered port.  Unable to activate port py26-numpy. Use 'port -f activate py26-numpy' to force the activation.
> Error: Failed to install py26-numpy
> Please see the log file for port py26-numpy for details:
>     /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-numpy/py26-numpy/main.log
> Error: The following dependencies were not installed: py26-numpy
> David-Laxers-MacBook-Pro:~ davidlaxer$ 

Why does /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/_methods.py already exist if it does not belong to a port?

Did you previously have this port installed, and then uninstall MacPorts? If so, how did you uninstall MacPorts?
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