New downloadable version of OxCal

[christoph...@rlaha.ox.ac.uk]

Those of you who use OxCal on your own computers will know that the features within Firefox which enabled this to work had been disabled and we were having to use an old version of Firefox and a special addon to make this work.

I have now found what I hope is a much better permanent solution which works with any browser.  The actual software version has not changed - this is just a different user-interface package.

The new method uses a software package NodeJs available from:

https://nodejs.org/

The distribution of OxCal now includes a file NodeServer.js which you run from node using the command line:

node NodeServer.js

This sets up a dedicated local web server for OxCal which enables you to use it as if it was on a server but accessing your own files.  As with the Firefox version, the program accesses whichever directory you wish to use for OxCal files.  Further details are given at:

http://c14.arch.ox.ac.uk/oxcalhelp/readme.html#local

including ideas on how you might set this up for a research group.  At the moment the system does not allow you to convert image files or generate multiple page prints, but I will try to add that later for those of you happy to install the necessary other software (Batik Toolkit and LaTeX).  The long-term aim is to make the downloadable and server versions to work in exactly the same way.

Please feedback any issues to this group.

Best wishes

Christopher

-------------

PS - the Firefox version is still available for download  at:

http://c14.arch.ox.ac.uk/oxcal.html#old

which includes instructions for installation of that version with Firefox.

[Charalampos Paraskeva]

Dear Christopher,

I'm running into problems with the Node.js version, as it does not work properly. I've followed the installation steps, run Node.js terminal and started the server, got to the first page and saved settings (the terminal window confirms settings saved), got to the interface page, then test run a date calibration (both from the mini interface and the proper Oxcal full editor) and it simply doesn't do anything. I can see in the .oxcal file only the line: Plot()  {R_Date("Test", 4500, 35); };, but no other values, which suggests that the binary file is not started/run for analysis. I've checked on Chrome, Firefox and IE11 on Windows 10 to no avail, checked that the Bitdefender Total Security is not the culprit (disabled all blocking actions, firewall, threat sense, etc.), it just doesn't seem to fire up the Oxcal binary and also it doesn't allow to change between views (Table, Single Plot, Multiple Plot, etc.), when you select any option it just refreshes the front page.

The idea is good, but I can't figure what went wrong. It's early days though, so understandable.

Best wishes,

Harry

[Christopher Ramsey]

As you say it is early days - and I was asking this group to test it for that reason. I'm sure we will be able to find the problem.

Yes - I have had another similar report - I think for some reason the executable file is not being run. Can I check a few details with you to try to work out what is happening.

1. If you look in the OxCal directory has it created a file called setup.json?

2. If you go to:

http://localhost:8080/setup.html

you should see the entry for 'OxCal binary'. If you copy that and then open the terminal and paste that in (when in a suitable working directory) you should see something like:

$ /Applications/OxCal/bin/OxCalMac
OxCal v4.3.2 (c) Bronk Ramsey (2017)
OxCal v4.3.2 Bronk Ramsey (2017); r:5
IntCal13 atmospheric curve (Reimer et al 2013)
>

which indicates that the executable is working. This is actually the same executable as in previous releases so there should not be a problem with this.

3. If you go to your normal OxCal working directory and paste in the same line but followed by Quick.oxcal - so something like:

$ /Applications/OxCal/bin/OxCalMac Quick.oxcal
OxCal v4.3.2 (c) Bronk Ramsey (2017)
$

you should just see the version number and then find that the files Quick.log, Quick.txt and Quick.js have all been updated.

4. Can you also check whether the program is able to see the file system correctly - so does [File > Manager] show the local file structure from within OxCal?

5. Finally - were you using a previous Firefox version of OxCal or is this the first time you have tried the downloaded version?

Many thanks for your help in sorting this out.

Also if anyone has success with their setup let us know. I have tested it most extensively on a Mac - but also under Windows 7 - not Windows 10.

Best wishes

Christopher

> --
> You received this message because you are subscribed to the Google Groups "OxCal" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to oxcal+un...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

[Charalampos Paraskeva]

To answer the question in aid of program development:

1. Yes the file is created and its contents agree to what was in the Setup screen.

2. I've browsed with CMD and with the terminal from Node.js to the binary and got the following:

(...)(...) - (...)
OxCal v.4.3.2 (c) Bronk Ramsey (2017)
>

3. Nope...that doesn't work. I get the following without creation of Quick.log, Quick.txt and Quick.js (it doesn't create them when run from the interface either):

(...)(...) - (...)

4. Yes the file manager and structure are there. See the following image:

5. I've been using various versions of OxCal since 2011. The latest stable version in use is 4.3.2 on Firefox 56 with addon. The latter runs smoothly without issues. The new method with Node.js something doesn't click. I've tried to see whether it is a node issue, but it successfully runs code from test .js files.

Hope these help!

[Christopher Ramsey]

Ok - that is very useful - clearly the OxCal executable is not picking up the source directory for the files - this is why you are getting (...)(...) - (...). I will email you off-group to ask some more specific questions.

Best wishes

Christopher

> On 17 Apr 2018, at 12:19, Charalampos Paraskeva <net...@gmail.com> wrote:
>
> To answer the question in aid of program development:
>
> 1. Yes the file is created and its contents agree to what was in the Setup screen.
>
> 2. I've browsed with CMD and with the terminal from Node.js to the binary and got the following:
> (...)(...) - (...)
> OxCal v.4.3.2 (c) Bronk Ramsey (2017)
> >
>
> 3. Nope...that doesn't work. I get the following without creation of Quick.log, Quick.txt and Quick.js (it doesn't create them when run from the interface either):
> (...)(...) - (...)
>
> 4. Yes the file manager and structure are there. See the following image:
>
>
>
>
>
>
>
>
>
>
>
>
>
>

[Bernd Kromer]

Dear Christopher

I installed the new version using nodejs successfully on Window 7, but on Windows 10 (64bit) I see the same behavior like Charalampos. Before I installed the new version, I calibrated one date (3000 +- 10) using the mini-interface in the old version, so a quick.js etc. was created in the old version. Now when I try to calibrate a date I get a plot of the 3000+-10, regardless of age. When I delete the quick.* it simply changes to the front page of OxCal.

Models run fine on Windows 7, but not on Win 10.

Hope this helps somewhat?

regards, Bernd

[Christopher Ramsey]

Bernd

I think I may have found the problem which is to do with the space in the "Program Files" directory name. I have tried to fix that and so if you download the package again you can see if that now works on your Windows 10. I think there must be change in what is treated as the first argument sent to an executable from Windows 7 to Windows 10.

Best wishes

Christopher

[Charalampos Paraskeva]

Indeed it was an issue with the rendering of the space character! I confirm that it is now fully functional on Windows 10 too. Thank you for your hard work!

All best,

Harry

[Christopher Ramsey]

Thank you for your help and quick feedback!

Best wishes

Christopher

[Josh Miller]

Dear Christopher,

Thanks for pulling this together. I'm looking forward to being able to use OxCal in this modified way.

Currently, the NodeServer.js system isn't working for me (Mac). OxCal loads on a variety of browsers, but when I try to calibrate a date, if get the following error:

"Error: ENOENT: no such file or directory, open '/Users/xxxx/OxCal/Quick.oxcal':Write failed to /mydata/Quick.oxcal"

[xxxx is my redaction]

Looking at some of the previous discussions, I can report the following (in case it is useful):

1. From within my OxCal folder, when I enter:

/Applications/OxCal/bin/OxCalMac Quick.oxcal

I get:

OxCal v4.3.2 (c) Bronk Ramsey (2017)

Segmentation fault: 11

The Quick.log, Quick.txt and Quick.js do all get updated (but I don't know what the segment fault is indicating).

2. Within OxCal, [File > Manager] is blank. I assume this means the program is not able to see the file system correctly?

Thanks for your thoughts!

-Josh

[Christopher Ramsey]

Sounds like it could be a permissions issue. Do you have the old Firefox version running on your machine. The OxCalMac binary has not changed and so should run the same on the command line.

You may want to check - are you running the nodejs system from the command line and is that where you see the error below? If so then the NodeJs system should be running as you on the system and files created and altered etc should have your name by them when you check the information. If the directory were readonly or owned by someone else - or if the node server was being run by another user that would cause a problem like this. The error message is just saying that it cannot create the Quick.oxcal file - is the version there new or one that was there before?

I am running this on a MacBook Pro running High Sierra and previously checked it on one running Yosemite. It is possible that the executable does not run on pre-64 versions but that should be no different from the Firefox version. Perhaps someone else has a similar experience?

Christopher

[Christopher Ramsey]

The other thing that you might check is that in neither your directory nor your setup file do you have a space either side of OxCal. This should work if you have it in both places but not only one. I can reproduce the error below by changing my user directory name to '/Users/xxxx/OxCal ' for example. The message indicates that nodejs is not able to read the directory or create a file for some reason.

Christopher

> On 26 Apr 2018, at 20:11, Josh Miller <mill...@gmail.com> wrote:
>

[Josh Miller]

Hi Christopher,

Thanks for your thoughts.

Indeed - I had a typo in the setting pointing to my home directory (sorry!)...

Working great!

Cheers,

-Josh

[Christopher Ramsey]

I have uploaded an update (30th April) which addresses an issue which was noticed with running longer models.  This was apparent with KDE_Model runs which are often long for large datasets - but may also apply to models which need to run for a long time for convergence to.

The symptom we were getting was the model quitting early.  I tracked this down to the way the calls were being treated in the NodeServer software.  

I suggest that you download an update.  The only file that has changed is the NodeServer.js so you can just replace that if you don't want to change your setup in any other way.  Otherwise just keep your setup.json file and put it into the oxcal directory after the installation.

Please let me know of any other issues that you come across.

Best wishes

Christopher

[Michael Berry]

Hi Christopher,
The node.js version is running fine for me on Windows 10 64 bit. The only problem I have encountered is that the Stratigraphic view doesn't seem to function any longer. That is, selecting Stratigraphic view does flip uniform phase/sequence models prior to running but after a successful run the graphic display defaults to Chronological view. 
Best,
Mike

[Christopher Ramsey]

There is a reverse order button just to the left of the dropdown for views above the plot/table which enables you to toggle this back and forth. Also available under [Format > Show > Style > Reversed]. This may not be linked to the code order anymore though - as I think it defaults to chronological on run.

Best wishes

Christopher

[1holli...@gmail.com]

Christopher,

I am new to this application ( A client needs OxCal loaded), I followed your readme.txt file and I cannot get it to work.

I am running Win7 (64-bit), I placed your files in "C:\Program Files\OxCal".

I Open a command prompt (Administrator) and change the directory to the above mentioned. I then type:"node NodeServer.json" and I receive the following:

Then I notice that the file does not have "on" on the end, so i try it without the "on" on the end. It still failed. I realized that maybe the port didn't have a rule for this app on the firewall. I created a rule on the firewall. I now get the application appearing in the browser. I had the user test and he received these errors:

The path is not the path I put in the settings. Is the above path a default one? Do I just create that path?

I will continue working on this, however any help would be greatly appreciated.  

[Christopher Ramsey]

It should be just js rather than json in the command:

node NodeServer.js

The user will also need write access on the setup run for this. They should then enter their working directory - which as a default will be the user's own directory /OxCal so in your case. The directory does already need to exist. They might be able to get it to work simply by creating the OxCal directory in their user area.

Christopher

> On 6 Jun 2018, at 15:32, 1holli...@gmail.com wrote:
>
> Christopher,
>
> I am new to this application ( A client needs OxCal loaded), I followed your readme.txt file and I cannot get it to work.
> I am running Win7 (64-bit), I placed your files in "C:\Program Files\OxCal".
> I Open a command prompt (Administrator) and change the directory to the above mentioned. I then type:"node NodeServer.json" and I receive the following:
>

> <Auto Generated Inline Image 1.png>

>
> Then I notice that the file does not have "on" on the end, so i try it without the "on" on the end. It still failed. I realized that maybe the port didn't have a rule for this app on the firewall. I created a rule on the firewall. I now get the application appearing in the browser. I had the user test and he received these errors:
>

> <Auto Generated Inline Image 2.png>

> <Auto Generated Inline Image 1.png><Auto Generated Inline Image 2.png>

[Thomas Dye]

Aloha Christopher,

This works very nicely on Linux.  Thanks!

All the best,

Tom