[Ifeffit] Macports ifeffit and Demeter Update
Schima, Frank
frank.schima at nist.gov
Tue Jul 15 09:36:58 CDT 2014
You simply type the complete name. I should have wrote that initially.
sudo port -f activate demeter-devel @0.9.20pre10_0
-Frank
On Jul 14, 2014, at 4:13 PM, Jennifer Carter <jwc137 at case.edu<mailto:jwc137 at case.edu>> wrote:
Frank,
Looks like I have two versions of demeter-devel installed
sudo port -f activate demeter-devel
Password:
---> The following versions of demeter-devel are currently installed:
---> demeter-devel @0.9.20-2014-06-06_0
---> demeter-devel @0.9.20pre10_0
Error: port activate failed: Registry error: Please specify the full version as recorded in the port registry.
How do I specify a the full version?
Thanks
Jennifer
[https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=ea034fd1-0125-4a6f-9531-0a82c40c5238]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 at case.edu<mailto:jennifer.w.carter at case.edu>
On Mon, Jul 14, 2014 at 3:00 PM, Schima, Frank <frank.schima at nist.gov<mailto:frank.schima at nist.gov>> wrote:
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 at case.edu<mailto:jwc137 at 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.
[https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=469920f1-a525-4ea3-96e5-780c6c639ac4]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 at case.edu<mailto:jennifer.w.carter at case.edu>
On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank <frank.schima at nist.gov<mailto:frank.schima at 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 at case.edu<mailto:jwc137 at 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$
[https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=65036228-9c54-447b-993a-c4ada3d12ec4]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 at case.edu<mailto:jennifer.w.carter at case.edu>
On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank <frank.schima at nist.gov<mailto:frank.schima at 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 at case.edu<mailto:jwc137 at 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
[https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=da579cbd-6543-4821-bd89-17fb33a6662e]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 at case.edu<mailto:jennifer.w.carter at case.edu>
On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank <frank.schima at nist.gov<mailto:frank.schima at 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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