[Ifeffit] "PCA not enabled" on Mac version of Demeter: Athena

[Ellen Daugherty]

Frank,

I apologize for not responding sooner, other urgent issues suddenly came up!

I followed Bruce's installation directions on the Demeter page (
http://bruceravel.github.io/demeter/) and the Xcode (
https://guide.macports.org/#installing.xcode) and Macports (
https://www.macports.org/install.php) installation instructions. I had
issues the first time I tried to install Demeter (i.e. text in Terminal
indicated things weren't proceeding successfully and it was taking a long
time), but the second time, it appeared to work.

I now am receiving the "command not found" response when trying to open the
Athena program in Terminal. I don't know why that didn't happen earlier.

Ellen

On Wed, Oct 8, 2014 at 3:55 PM, Schima, Frank <frank.schima at nist.gov> wrote:

>
>
>  On Oct 7, 2014, at 5:08 PM, Ellen Daugherty <daughertyee at gmail.com>
> wrote:
>
>  Bruce and Frank,
>
>  In response to Bruce's suggestion:
>
> A simple way to test from the command line whether the modules can be
> loaded is to do
>
>    perl -e 'use PDL::Lite'
>
> My output is:
>
> "Can't locate PDL/Lite.pm in @INC (@INC contains:
> /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16
> /Network/Library/Perl/5.16/darwin-thread-multi-2level
> /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2
> /System/Library/Perl/5.16/darwin-thread-multi-2level
> /System/Library/Perl/5.16
> /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.16 .) at -e line 1.
>
> BEGIN failed--compilation aborted at -e line 1."
>
>  In response to Frank's suggestions:
>
>   $ port installed perl5
>
>   My output is:
>
> -bash: port: command not found
>
>   And for,
>
>   $ echo $PATH
>
>   My output is:
>
> /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
>
> Does this mean that there is a problem with the Macports location?
>
>
>  It means your path is not setup to find Macports. It says nothing about
> if Macports is installed or not. So when you run “perl” you are using the
> OS X perl and of course that won’t work. Now I’m really curious. Given
> this, how did you install the demeter-devel port and how are you actually
> running demeter programs? You would have encountered the same “command not
> found “ errors unless your path was correct like mine is.
>
>
>  -Frank
>
>
>  Thank you!
>
>  Ellen
>
> On Tue, Oct 7, 2014 at 2:18 PM, Schima, Frank <frank.schima at nist.gov>
> wrote:
>
>> On Oct 7, 2014, at 1:29 PM, Bruce Ravel <bravel at bnl.gov> wrote:
>>
>> On 10/07/2014 02:43 PM, Schima, Frank wrote:
>>
>> I’m going to need specific steps to reproduce the issue.
>>
>>
>> As I understood the issue from Ellen's first message, the problem is that
>> Athena is not able to find the modules "PDL::Lite" (which should be
>> installed when "PDL" is installed) and/or "PDL::Stats::GLM".
>>
>> If I force Athena to fail to load one of them, then selecting "Principle
>> Components Analysis" from the main menu will look like the first attachment.
>>
>> If Athena can find those two modules, the selecting "Principle Components
>> Analysis" will look like the second attachment.
>>
>> The test in Athena is really simple.  If those two modules can be loaded
>> successfully, then the PCA tool will display properly.  If not, that
>> message is the graceful fall back.  My guess is that one or both of those
>> perl modules is not being found on Ellen's computer.
>>
>> A simple way to test from the command line whether the modules can be
>> loaded is to do
>>
>>    perl -e 'use PDL::Lite'
>> or
>>    perl -e 'use PDL::Stats::GLM'
>>
>> If they cannot be found, then perl spits up an error message.  If  they
>> can, then nothing happens.
>>
>>
>>  Nothing happens for me. So they are installed. At this point it looks
>> like an issue with her Macports install.
>>
>>  I would start by verifying that she is correctly using perl 5.16 in
>> Macports. What is the output of the following?
>>
>>  $ port installed perl5
>>
>>  Here is my output.
>>
>>  The following ports are currently installed:
>>   perl5 @5.12.4_0+perl5_16 (active)
>>
>>  Then the Macports perl needs to be in your path. What is the output of
>> the following?
>>
>>  $ echo $PATH
>>
>>  My output is:
>>
>>
>> /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
>>
>>
>>  Cheers!
>> Frank
>>
>>
>> B
>>
>> --
>> Bruce Ravel  ------------------------------------ bravel at bnl.gov
>>
>> National Institute of Standards and Technology
>> Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
>> Building 535A
>> Upton NY, 11973
>>
>> Homepage:    http://bruceravel.github.io/home/
>> Software:    https://github.com/bruceravel
>> Demeter:     http://bruceravel.github.io/demeter/
>> <pca_wrong.png><pca_right.png>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
>   _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20141016/8a85f73f/attachment.html>