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 Forum index » Advanced Topics » Additional Software (PETs, n' stuff) » Engineering/Science/Simulation
R - statistics package and scripting language
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emil

Joined: 10 Nov 2009
Posts: 618
Location: Austria

PostPosted: Fri 28 Jan 2011, 03:48    Post_subject: Java  

I think the official Java installs also to /mnt/home

It is possible that some link is broken but please try
http://sage.math.washington.edu/home/emil/sagelive/jre_1.6.0_22.pet
Sounds like great stuff Very Happy
emil
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Fri 28 Jan 2011, 04:35    Post_subject:
Sub_title: The R-puppy commeth...
 

Thanks again, emil!
I've downloaded and will try again with a java remaster. And research manual remastery shortly if that flunks. The puplet is rather large - >700Mb R + Rcmdr + java + firefox + KDE (+CowLog + ImageJ) which surprised me a little. (Just goes to show the genius in getting the base model Puppies so small.) Will look at streamlining too, re your earlier request,

Cheers!

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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Sun 30 Jan 2011, 20:06    Post_subject:
Sub_title: R-puppy now possible
 

Very Happy

emil - your pet certainly did the trick! Java (jre 1.6.0_22) is now 'embedded' in the remastered lupu_520.sfs, and together with your R+Rcmdr SFS (or pets - I tested it both ways) AND using pa_mcclamrock's "Remasterpup3" a puplet can be easily constructed running R, JRE and ImageJ straight from the live-CD.

I still ran into trouble with the java frontends for R (e.g., rJava and RImageJ packages) - but it turns out I 'just' needed the SDK (java_ee_sdk-5_01-linux.bin, 134MB - and from what I read from non-Puppy linux forums the SDK is needed to properly install JGuiR). Newbie question - from what I understand I shouldn't need to install JDK and the JRE pet - is that correct? I can't spend more time for a few weeks on testing that and getting R and ImageJ properly coordinated - it's more important to actually use the new CowLog/KDE/Rcmdr toolbox.

One final noob question if you wouldn't mind: I prefer to use wBAR for desktop organisation but can't work out what file to link to the R 'plug-in' that actually starts R - just like the existing menubar. Could you give me a clue for that please - I hope I don't have to write a startscript somewheres, although that would be the alternative,

3 Cheers!

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emil

Joined: 10 Nov 2009
Posts: 618
Location: Austria

PostPosted: Sun 30 Jan 2011, 22:25    Post_subject:  

Hi Puppyt,

nice to hear it's going well Very Happy !
I am sorry, I cant give advice on SDK/Java. Thats out of my comfort zone!
I never used those.

I also have never used wbar, but after googling i found this thread
http://www.murga-linux.com/puppy/viewtopic.php?p=127662
and it seems to me that the contents of the wbar is stored in the hidden file /root/.wbar
it should have a fairly obvious syntax. Compare it to the file
/usr/share/applications/R.desktop
it should be possible to generate an entry for R in your wbar that way (with texteditor)

good luck and success for your work withanimal research, and it would be perfect if you could keep us posted on any experience with your statistic pupplet!
Cool emil
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Wed 02 Feb 2011, 22:34    Post_subject:
Sub_title: R-puppy possible
 

G'day again emil -

Strange - I posted a quick note yesterday but it seems to have got lost in the ether...
In short - I've got Lupu 520 remastered with your R/Rcmdr SFS and java pet, with ImageJ, Kommander and CowLog all working happily. I dipped into the Ubuntu repositories quite a bit for the Kommander and KDE dependencies. The iso came in at about 480 MB with Firefox pre-configured with Zotero etc.
The Java SDK - needed for various R packages and a foundation for JGuiR - was definitely a bridge too far for a meddling muddler like myself, so no go there.
I even wrote a startscript so that CowLog can be run from a desktop icon or wBar. I had R listed in the wBar but it broke - often - I think the main issue is with the official wBar_1.3.3_setup (?) pet and that has attracted concern elsewhere in the Puppy forum recently. But you're right, a manual edit of the wBar config files should be the way to move forward with that particular decoration.

Have you come across this R-gui before http://www.red-r.org/? I haven't tried it yet, and it looks extremely slick for an open source project. I wonder whether it might be an alternative to RCmdr for budding statisticians?

Many Thanks Smile

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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Thu 03 Feb 2011, 00:05    Post_subject:
Sub_title: Rkward
 

THIS IS NOT A URGENT REQUEST otherwise I would start a new thread in the 'Pets' section of the forum. More of a wistful wish...

Embarassed OK I did it again - a quick google suggested that RKWARD would be a useful inclusion with RCmdr, for an R-learner's puplet. Forgot to mention earlier that I'm using KDE 3.5.10 for stability. (AFAIK - I'm only new to KDE too.)
Not finding an Rkward deb in PPM with Ubuntu-main and ubuntu-universe, I downloaded rkward_0.4.9c-1_lenny_386.deb from Sourceforge and a dependency check after install showed "all clear". All went extra smoothly up to this point - but a menu entry couldn't be created and all my other attempts to start Rkward have failed. Glancing through the various scripts it seems that the install didn't go perfectly as it is looking for R in the wrong place.

Would anyone other than emil care to have a shot at compiling a Rkward pet (for either KDE 3 or KDE 4)? There's been a few times on this thread emil has been trying to get back to the real world - but we just keep dragging him back...

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emil

Joined: 10 Nov 2009
Posts: 618
Location: Austria

PostPosted: Thu 03 Feb 2011, 03:15    Post_subject:  

Hi PuppyT,
thanks, Realworld is mostly fine, and I can't feel any drag beside my own.
I looked at the 2 other Guis you mentioned. I won't mess with them, since they need Qt and RKWard also needs KDE.

About the questions with the Java development Kit. You dont need both, JDK or JRE is enough. If you install the "bundle package" for a possible remaster I would suggest the /opt/ directory (And quite some space in the save file, I recall like 300 MB?) Then you have the JDK executables in /opt/jdk-xxxxx/bin.
In order to work properly you have to add that directory to your path. You can test it manually in console with
Code:
export PATH=/opt/jdk-xxx/bin:$PATH

and then type java
If you want to permanently include that path in your remaster you can edit the textfile etc/profile in line 3
Cool best
emil
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Thu 03 Feb 2011, 21:45    Post_subject:  

Most Appreciated! Thanks, emil - will let you know if things go astray with your SFS and pet, but it's knitted together very well indeed in Lupu520. It even works without changing the SFS name as I posted earlier.
Cheers!

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emil

Joined: 10 Nov 2009
Posts: 618
Location: Austria

PostPosted: Fri 04 Feb 2011, 06:08    Post_subject: Rkward  

PuppyT, just one thought,
if you checked the installscripts, why don't you try to add a symlink at the place the scripts are lookin for R?
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Thu 10 Feb 2011, 02:18    Post_subject: Re: Rkward  

emil wrote:
PuppyT, just one thought,
if you checked the installscripts, why don't you try to add a symlink at the place the scripts are lookin for R?

Apologies for my late response emil, and thank you for the suggestion. I'm afraid that symlinks are waaaaay out of my league. In fact, practically anything object oriented starts to mess with my head. I regret that I've had to leave it for now due to sickness and work commitments, but I'll be keeping tabs with this thread and other R-puppy developments as they might emerge.
Do you have plans to retro-fit your pets/sfs into Puppy4? Is there an easy way a newbie could convert the SFS reliably to do that without YOU having to do the hard yards again?
Back to bed for me - at 4pm (groan)

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emil

Joined: 10 Nov 2009
Posts: 618
Location: Austria

PostPosted: Thu 10 Feb 2011, 03:17    Post_subject:  

Hi PuppyT,
sorry to hear that you are ill Sad - get well soon!
About symlinks - actually there is not so much object orientation in it, basically those are just signposts that lead to the right file, its entirelly a filesystem technique.

So example: The rkward installer is looking for /usr/bin/R but you have R installed in /opt/R-2.12.1/bin/R. Then you can place a Symlink like
Code:
ln -s /opt/R-2.12.1/bin/R /usr/bin/R

Optionally you can also use the Rox Filemanger to create such a link.
If the rkward script looks for R in /usr/bin it finds the link (signpost to /opt/..), there it finds R and voila, the script is happy and hopefully it works.
If this is practical depends if the install script is readable and you can identify the necessary symlinks (also their number). Another option is to add the appropriate R directories to your paths.

About R for Puppy 4. I don't know if it works, but if not than it is easiest in my opinion to recompile following the cookbook in this thread. Question Maybe it is also necessary to install a new version of iconv in Puppy 4 (was an additional dependency in the puppy 4 version las year).

So I wish you success with your work and good health,
best to Australia from Austria

emil
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flan

Joined: 06 Mar 2011
Posts: 1

PostPosted: Sun 06 Mar 2011, 05:30    Post_subject:  

PuppyT and Emil,

I'm a public health student who has a need for learning statistical modeling. I realize that folks like you don't get enough praise for your contributions. Thank you both for your time and energy! PuppyT, your vision of an R suite for students is beautiful! With only a very rudimentary understanding myself, I can only cheer on the sidelines here. As a relative newbie who has dabbled with a number of R GUIs, I found Rkward to be the most compelling; that would be so cool if rkward was part of your pupplet!
Please do post on here whenever your R statistical pupplet get unleashed.

Thanks again, Flan
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Mon 07 Mar 2011, 17:09    Post_subject:  

Cheers Flan -
Welcome to the Kennels!
I'm certain that emil has given me the recipe in his earlier messages for getting Rkward running in this little project - I simply haven't been able to get back to it with Uni and work pressures of late. I'll give it a red-hot crack again this weekend and let you know how it goes. Perhaps I could put it on a server somewhere for limited downloads - I wouldn't be game to 'release' it as a puplet. Won't have the Zotero stats help files, bookmarks, tutorials etc for beginners in Statistics unfortunately. That aspect is still a work in progress. Many Thanks for your interest, but I'm really just riding on emil's coat-tails and his inspiration. Smile

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Puppyt

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PostPosted: Sun 13 Mar 2011, 17:38    Post_subject:
Sub_title: R-puppy progress
 

No dice yet with RKWard-
First I used hondasid's Barebones 5.01 (http://www.murga-linux.com/puppy/viewtopic.php?t=64480) in the interests of getting a basic "R-puppy" base. emil's R+Rcmdr SFS worked, and I installed dejan555's minimal KDE libraries without problem (3.5.9: http://murga-linux.com/puppy/viewtopic.php?t=41115). I loaded kommander_3.5.10-0ubuntu1_i386.deb from a website archive somewhere and it worked, as did the CowLog_1.0-1.deb. However, no amount of symlinking (and rkward.bin tweaking) got me anywhere other than a brief flash of the 'RKWard' title dialogue before it dropped out.
Then I did the same with my larger working project (Lucid 520, without dejan's KDE but with 4.something KDE dependencies automatically downloaded from the Ubuntu repositories) and had the same result with attempting RKWard.
Finally I attempted dejan's KDPUP-lite puplet (puppy 484: http://www.murga-linux.com/puppy/viewtopic.php?t=55301) in case my KDE environment was impaired in some way (all dependency checks were OK for all packages) and couldn't get emils' Puppy5-compiled R+RCmdr SFS or pets to load properly. (emil - I forgot to try the updated iconv)
Sorry Flan - I'll have to make a formal request if anyone - with actual programming expertise, no numbkins like myself - could manage to construct a working RKWard pet for Puppy5 Sad

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emil

Joined: 10 Nov 2009
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PostPosted: Mon 14 Mar 2011, 06:32    Post_subject:  

Hello all,
unfortunatly I cant help much in getting rkward to work (have to run my business, so no time). But I noticed that rkward expects R to be compiled with "shared libraries enabled"
see http://rkward.sourceforge.net

I haven't compiled R explicitly with this option, so it might be that this is part of the problem.
There should be a library libR.so somewhere.

PuppyT, your approaches look very promising, if libR.so is missing, try to recompile R with the option --enable-R-shlib.

just my 2 cents, good luck - I am very happy to see this forum section is alive Smile
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