Your setup got munged somehow. You need to do what it says. Namely:

sudo port -f activate demeter-devel

-Frank

On Jul 14, 2014, at 3:55 PM, Jennifer Carter <jwc137@case.edu> wrote:

when I run 

sudo port activate demeter-devel @0.9.20pre10_0

--->  Computing dependencies for demeter-devel

--->  Activating demeter-devel @0.9.20pre10_0

Error: org.macports.activate for port demeter-devel returned: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port.  Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation.

Please see the log file for port demeter-devel for details:

    /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_demeter-devel-0.9.20pre10_0_54f3f2fd9281aa66df973ff2918ccf4354f1f896e5b2bc57d680266a42be52f1-5435/demeter-devel/main.log

Warning: Failed to execute portfile from registry for demeter-devel @0.9.20pre10_0

--->  Activating demeter-devel @0.9.20pre10_0

Error: port activate failed: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port.  Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation.

ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jennifer L.W. Carter

Assistant Professor
Department of Materials Science and Engineering
Case Western Reserve University

500B White Building

10900 Euclid Ave.
Cleveland, OH 44106-4901
phone: (216) 368-4214
email: jennifer.w.carter@case.edu

On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank <frank.schima@nist.gov> wrote:

For whatever reason, you do not have any version of demeter-devel active. You must activate the latest version as follows:

sudo port activate demeter-devel @0.9.20pre10_0

-Frank

On Jul 14, 2014, at 3:43 PM, Jennifer Carter <jwc137@case.edu> wrote:

Frank,

This is what I get for the following terminal inputs:

169-231-92-234:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel

The following ports are currently installed:

  demeter-devel @0.9.20pre10_0

  demeter-devel @0.9.20-2014-06-06_0

  ifeffit @1.2.11c_0+gcc48

  ifeffit @1.2.13_0+gcc48 (active)

  p5.16-ifeffit @1.0.0_0

  p5.16-ifeffit @2_0 (active)

169-231-92-234:~ jwc137$ ls -l /opt/local/bin/athena

ls: /opt/local/bin/athena: No such file or directory

169-231-92-234:~ jwc137$ ls -l /opt/local/bin/atoms

ls: /opt/local/bin/atoms: No such file or directory

169-231-92-234:~ jwc137$ 

ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jennifer L.W. Carter

Assistant Professor
Department of Materials Science and Engineering
Case Western Reserve University

500B White Building

10900 Euclid Ave.
Cleveland, OH 44106-4901
phone: (216) 368-4214
email: jennifer.w.carter@case.edu

On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank <frank.schima@nist.gov> wrote:

Jennifer,

There is nothing else to do. 

What is the output of the following 3 commands?

port installed ifeffit p5.16-ifeffit demeter-devel

ls -l /opt/local/bin/athena

ls -l /opt/local/bin/atoms

Here is the my output (on 2 different computers):

$ port installed ifeffit p5.16-ifeffit demeter-devel
The following ports are currently installed:
  demeter-devel @0.9.20pre10_0 (active)
  ifeffit @1.2.13_0+gcc48 (active)
  p5.16-ifeffit @2_0 (active)

$ ls -l /opt/local/bin/athena
lrwxr-xr-x  1 root  admin  43 Jul 14 10:53 /opt/local/bin/athena -> /opt/local/libexec/perl5.16/sitebin/dathena

$ ls -l /opt/local/bin/atoms
lrwxr-xr-x  1 root  admin  45 Jul 14 10:53 /opt/local/bin/atoms -> /opt/local/libexec/perl5.16/sitebin/atoms-gui

As for that perl command, make sure you are using Macports perl. 

$ which perl
/opt/local/bin/perl

-Frank

On Jul 14, 2014, at 2:47 PM, Jennifer Carter <jwc137@case.edu> wrote:

Frank,

I followed the instructions for updating a current version, but now when I type "athena" or "atoms" in the terminal I get the message "command not found" am I missing a step?

running  perl -e 'use Demeter; print $INC{"Demeter.pm"}, $/' 

indicates that nothing was installed.

Thanks

Jennifer

ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jennifer L.W. Carter

Assistant Professor
Department of Materials Science and Engineering
Case Western Reserve University

500B White Building

10900 Euclid Ave.
Cleveland, OH 44106-4901
phone: (216) 368-4214
email: jennifer.w.carter@case.edu

On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank <frank.schima@nist.gov> wrote:

Mac OS X users,

Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported. 

To update from your current version type the following:

sudo port selfupdate

sudo port upgrade outdated

To install from scratch after installing Macports [1]:

sudo port selfupdate

sudo port install demeter-devel

When done, your should see the following ports installed:

$ port installed ifeffit p5.16-ifeffit demeter-devel
The following ports are currently installed:
  demeter-devel @0.9.20pre10_0 (active)
  ifeffit @1.2.13_0+gcc48 (active)
  p5.16-ifeffit @2_0 (active)

Please reply to the list (NOT to me directly) about how this works for you. 

Cheers!

Frank

[1] <https://www.macports.org/install.php>

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