Trouble with R and .ged file

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Marc Gingold

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Sep 29, 2021, 10:23:36 AMSep 29
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Hi !
With visone 2.20 / Java 8 on Mac High Sierra :

When I want to install the required R libraries :
   Cannot run program "R": error=2, No such file or directory
   /usr/local/bin/R can run !

When I wan to open an existing .ged file
Failed to open a ged file:

Help me ! Thanks in advance,

Müller Julian

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Oct 3, 2021, 3:59:19 PMOct 3
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Hi Marc,

> When I want to install the required R libraries :
> Cannot run program "R": error=2, No such file or directory
> /usr/local/bin/R can run !

If visone can't find R by itself, you can tell visone the path to the directory of your R instance in the settings. The settings are accessible from the main menu via file -> options... The third tab in the settings dialog is used to configure the path to your R instance. Don't forget to check the radio button for "use external R instance" if you specify a path there.

> When I wan to open an existing .ged file
> Failed to open a ged file:

Well, I just tried to load some example ged file from the Internet and that worked just fine.
So you will have to provide me with a (preferably small) ged file that fails to open so that I can investigate what the problem is.
If you don't want to share such a file on the mailing list, you can send an e-mail directly to me (julian....@gess.ethz.ch).
If that is not doable for you, you will at least have to tell me what error messages visone writes to its debug console (accessible at the console icon from the toolbar at the top) so that I can at least get some idea what might be going wrong in your file.

Best,
Julian

Marc Gingold

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Oct 4, 2021, 9:20:59 AMOct 4
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Hi Julian,
Thanks for the answer.

With a small ged file, I could open it. Not with a big one (12 000 persons) :
"Failed to open file xxxx.ged". Is there a size limit ?
There are some genealogical errors in it.

Besides, I always have the R-problem.

Best,

Marc Gingold
:-O Wissen ist Macht!  8-( Ich weiß nichts. ;-> Macht auch nichts.


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Geny_PierreSigisbert_all.ged
Downloads_—__usr_local_bin_R_—_R_—_81×19_et_Install_R_packages__Rserve_igraph_et_configuration_et_visone.jpg

Müller Julian

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Oct 5, 2021, 10:01:29 AMOct 5
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Hi Marc,

> With a small ged file, I could open it. Not with a big one (12 000 persons) :
> "Failed to open file xxxx.ged". Is there a size limit ?
Not that I'm aware of.

> There are some genealogical errors in it.
That is more likely to be the problem. Visone performs a fairly complex operation to load ged files: It first converts ged files to graphml internally, and then actually loads the graphml data. Any of these two steps could fail if there is some unexpected structure in the data.
To investigate what's going wrong, I need a file that fails to load. The one you attached to the previous e-mail loads successfully (as far as I can tell), so it doesn't really help.
Since it's a large file, you can send it to me privately (julian....@gess.ethz.ch), preferably compressed.

> Besides, I always have the R-problem.

Did you try checking the "use external R instance" box? Otherwise, visone ignores the path you specify there (and instead assumes that R is available from a directory specified in the PATH environment variable).
If that doesn't work, /usr/local/bin probably contains just a link to the R executable. You could also try to enter the path to the actual R directory there.

Best,
Julian

Marc Gingold

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Oct 6, 2021, 6:16:11 AMOct 6
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Hi Julian,

I have the "failed to open" with the following file.
And always the same problem with R.

Best,

Marc Gingold
:-O Wissen ist Macht!  8-( Ich weiß nichts. ;-> Macht auch nichts.
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marcgingold_—__Library_Frameworks_R_framework_Resources_bin_R_—_R_—_80×22_et_Install_R_packages__Rserve_igraph_et_configuration_et_visone.jpg
Geny_PaulAlbert.ged

Müller Julian

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Oct 6, 2021, 1:20:02 PMOct 6
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Hi Marc,

I could reproduce that the ged file doesn't load and implemented a bug fix.
You can download a corrected version of visone from here: https://polybox.ethz.ch/index.php/s/Ek5WF8gVCsOwHO4
(or if for some reason you like the new zip bundle version more: https://polybox.ethz.ch/index.php/s/IkzRQ2sLdqNssnj)
While I was at it, I also made sure that visone now correctly recognizes the file's encoding. That means accents in names should no longer be broken.

That said, the file you sent me will still not load as-is, since it is not a valid ged file as far as I can tell. I don' t think line 7897 is valid syntax. After deleting this line, visone manages to load the file.

If you encounter any other failures when loading ged files, you can also start visone from the terminal and check what it writes to the console while the file is getting imported. That should usually tell you where visone abandons loading the file.

Regarding your R issue, I honestly can't reproduce it, but I'm running visone on Windows and visone must use a different strategy to find R on that OS. I will try to reproduce the problem on macOS tomorrow with the help of a colleague, and will get back to you afterwards.

Best,
Julian

Müller Julian

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Oct 8, 2021, 6:32:17 AMOct 8
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Hi Marc,

Going back to your R problem, I have a suspicion what the problem is.

First of all, /usr/bin/local is apparently not on the PATH in Java on macOS, so we have to tell visone the path to the R executable manually.

Second, you should go to visone's R settings.
Change the path to R to: /usr/bin/local/ (there is a bug there when entering the path manually, so I suggest to use the "browse" feature to set the path)
Then check "Use external R instance:"
Then click on "apply" at the bottom left of the dialog, otherwise visone will not save and apply the new settings.

After doing all these steps, you should be able to run R and install all the required libraries from inside visone.

Best,
Julian

Marc Gingold

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Oct 10, 2021, 9:24:44 AMOct 10
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Hi Julian,

It works when I remove the few lines like you indicated ( ^Proprietaire ).
I had to split the family tree.
Because visone does not accept fully more than 10,000 nodes. And I get a memory exhaust even when I choose the simplified node.

For the R problem : After some relaunch, I I succeeded with the full path :

echo $PATH

/Library/Frameworks/R.framework/Versions/3.6/Resources/bin:/usr/local/opt/....


A general hint for networks :

I suggest to animate the graphs with time :


For genealogical trees : the growth along the years ...

and a variant when the fallen leaves are deleted (deaths)


For the publications of an "old" laboratory to see the collaborations evolving over the years (internal or external authors). Each link represents a common written paper.


Thanks for all,


Best 


Marc Gingold
:-O Wissen ist Macht!  8-( Ich weiß nichts. ;-> Macht auch nichts.

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