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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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loserguy

Joined: 08 Mar 2010
Posts: 2

PostPosted: Mon 08 Mar 2010, 05:58    Post subject:  

I use command line for R mostly, but drop back to GUI when I'm trying to sell an idea. JGR (http://jgr.markushelbig.org/JGR.html) is nice but needs Java.
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hayden


Joined: 13 Sep 2006
Posts: 63
Location: New Hampshire USA

PostPosted: Sun 26 Dec 2010, 21:57    Post subject: Learning R
Subject description: resources for beginners
 

For anyone who wants to LEARN R you can access the examples I created for my two-semester intro. stats. sequence at

http://courses.statistics.com/software/help.php

which also has limited support for Rcmdr. This is for beginning statistics students who are not programmers. There are links to the example datasets so you can follow along..

If you want more detail I recommend the book on using R in an intro. course by John Verzani. This is for statistics users and professors whereas most of the official R documentation is for programmers. There is a UsingR package to go with Verzani's book
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emil

Joined: 10 Nov 2009
Posts: 616
Location: Austria

PostPosted: Fri 31 Dec 2010, 17:46    Post subject: R-2.12.1
Subject description: including R Commander, build in lupq-511
 

2 Pets Cool : R and R + Rcmdr



Those were build in Lupu Quickset Edition 511.

Dependencies:
gfortran-4.4.3
recommended/optional:
devx.sfs (to install and compile additional packages)
tcltk8.5 (graphical download menu packages needs it)
Xorg-high.pet (from Quickpet for 3d plots)

Download location
http://boxen.math.washington.edu/home/emil/MathSoftware/Puppy5


Just R: for those who just need commandline: start with R from terminal, installs normal
Rcmdr: R + Rcmdr, for those who like a gui. R - starts just R in terminal, Rcmdr starts R + Rcmdr, has also menu entries in Menu/Business/Calculate, installs to /mnt/home

maybe those work also in other puppies, but I am not sure. Test reports welcome Very Happy

Happy 2011
emil
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hayden


Joined: 13 Sep 2006
Posts: 63
Location: New Hampshire USA

PostPosted: Fri 31 Dec 2010, 21:23    Post subject:  R 2.12  

I booted vanilla Puppy 511 from a CD. (It might have grabbed some previously saved files off my system at boot.) Then I installed gfortran and R 2.12. It worked great! Including graphics this time round. A good test if anyone is playing with this is (on the R command line)
Code:

demo(graphics)

There are no menus on the windows so if you want to save or print a graph you have to do that from the command line.

Code:

library()

will list the 27 packages already installed along with R.

Thanks, emil
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hayden


Joined: 13 Sep 2006
Posts: 63
Location: New Hampshire USA

PostPosted: Fri 31 Dec 2010, 22:05    Post subject:  Rcmdr  

Booted the same 511 but took care not to load any files not on the CD. Then I installed emil's gfortran, tcl/tk and Rcmdr pets. Seemed to work fine. I will try some older Puppies next year.
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hayden


Joined: 13 Sep 2006
Posts: 63
Location: New Hampshire USA

PostPosted: Fri 31 Dec 2010, 23:54    Post subject:    

After playing around with R and Rcmdr I remastered Puppy with those installed. The CD boots and R and Rcmdr are on the menu but neither runs from either the command line or the menu. It looks like a window opens and instantly closes. No error message.
Code:

# cd /usr/bin
# ls R*
R  Rcmdr  Rcmdr.sh  R.sh
# more R.sh
#!/bin/sh
# this starts R and calls the start script /root/.Rprofile
# which starts Rcmdr
xterm -e /mnt/home/R-2.12.1/bin/R --no-init-files.

I see two problems. /mnt/home does not exist. Earlier that was the thumb drive on which the pet was stored. However, that thumb drive does not have a R-2.12.1 directory on it anyway. Then .Rprofile does not exist in /root. (I did ask that hidden files be shown and did see some others.)
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emil

Joined: 10 Nov 2009
Posts: 616
Location: Austria

PostPosted: Sat 01 Jan 2011, 00:17    Post subject:  

Hmm, will look at it, *sigh*
emil
oh, first thought, I guess anything in mnt/home will not be remastered with the standard scripts.
I plan to put it into an sfs and make something like a math.sfs (with maxima and octave), but I don't promise
If you want to make a remastered lupq 511 with R then I suggest to compile fresh, i.e. install, tcltk and gfortran, load the devx, then load the r sources and do vanilla (./configure, make, install) hmm loading the R.pet should be the same.
then follow my instructions for getting R commander installed from earlier this thread (should be something like install.packages(Rcmdr, dependencies=true)
that should work,
emil
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emil

Joined: 10 Nov 2009
Posts: 616
Location: Austria

PostPosted: Sat 01 Jan 2011, 07:36    Post subject: Other puppies  

Just tried it in Wary (102) and spup (first release), it didn't work Crying or Very sad
So atm restricted to Ubuntu puppies.
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hayden


Joined: 13 Sep 2006
Posts: 63
Location: New Hampshire USA

PostPosted: Sat 01 Jan 2011, 11:31    Post subject: R 2.12 not persistent  

Why does something get mounted on /mnt/home? Usually apps end up in one of the /bin folders or occasionally in the user's home directory (/root for Puppy). It appears that R gets installed to a RAM image of /mnt/home? After I booted from the CD and installed R, /mnt/home was the thumb drive the pet had been on. Of course thumb drives should not get normally included in a remaster. However, it looks like R did not get put on the physical thumb drive anyway. I can't find it there now, nor can pfind find it anywhere from the remaster with that thumb drive mounted.

I am hoping that losing the dot configuration file is not a problem and that R would run with defaults if that cannot be found. I've never quite figured out what configurations get saved in a remaster. I always choose to have the remaster NOT save settings for my hardware as the point of the remaster is to give it to students to use on their own computers.

There is an older R 2.4 out there -- a dot-pup I think. I believe that DID survive a remaster. Maybe there are some clues in that. Maybe I can get that to work in a Puppy that also has a development environment available so I could install R packages. I went through all this a year or two back based on Puppy 2.14 and I think the roadblock was installing R packages.
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hayden


Joined: 13 Sep 2006
Posts: 63
Location: New Hampshire USA

PostPosted: Sat 01 Jan 2011, 16:18    Post subject: Update on R-2.4  

Back in 2008-2009 I built a couple of ISOs for something I called "SciPup" that could be handed out to college students in science. One was based on Puppy 2.14 and the other on TeenPup (which was also based on 2.14). I just booted both of those and R did indeed make it into the remaster. The R files seem to be in /usr/lib and /usr/bin. I did not see a dot configuration file. The run script is longer than _War and Peace_ but seems to be mostly generic stuff that came with the source. If anybody messes with this I seem to recall that R tried to find the Mandrake C-compiler if you tried to install R packages. I do not have ANY C compiler installed in SciPup. I don't think there was a developer sfs back then, and I'm not sure if there is one now for Puppy 2.14. If so I think one could edit Mandrake out of the startup shell script.

One other thing I learned is that these older pups do not boot up from my SATA CD drive;-( I had to try them on other hardware.
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emil

Joined: 10 Nov 2009
Posts: 616
Location: Austria

PostPosted: Sun 02 Jan 2011, 12:35    Post subject: remaster Rcmdr  

hi hayden,
The /mnt/home was used intentionally by me when building by giving the ./configure prefix=/mnt/home option. The advantage is that it doesn't use up your savefile (300 MB), disadvantage is remaster won't work.

To fix it you could ask the students to install the pet themself (which is not so hard) or you install just the R package and then install Rcmdr from within
Code:
install.packages("Rcmdr", dependencies=TRUE)


emil
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hayden


Joined: 13 Sep 2006
Posts: 63
Location: New Hampshire USA

PostPosted: Sun 02 Jan 2011, 13:44    Post subject: R  

OK. I'll continue to work with the R 2.4 package. The point for students was to avoid having to install things. Most are Windows users and might as well just install R for Windows and avoid all these issues;-) And to install their own R packages in Puppy they would need the developer package while the Windows packages are precompiled.

Rcmdr seems to have grown to require roughly 150 other packages. That is why it inflates the save file by 300Mb. I will try to find the Rcmdr that goes with R 2.4. I think Rcmdr used to have about 10 dependencies. My guess is that it has added many capabilities that would not be needed in a basic stats. course anyway.

Thanks for you efforts re R 2.12. This may be good for me to use if not for students.
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emil

Joined: 10 Nov 2009
Posts: 616
Location: Austria

PostPosted: Sun 02 Jan 2011, 13:57    Post subject:  

I ment if you install just R.pet (this is in the savefile) with devx.sfs and dependencies installed, then you could install Rcmdr inside the remastered filesystem and afterwards do a remaster. I just did this and it worked, however you probably will have to remove /root/.rProfile and /root/.rHistory manually. If you use a normal lupu 5.11 as base than you could give the students a Rcmdr puppy.

Either way, thanks for the pointer with the R plotting, Ill try to make this work in sagelive
emil
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Puppyt

Joined: 09 May 2008
Posts: 567
Location: Gatton, Queensland

PostPosted: Tue 18 Jan 2011, 00:18    Post subject: R-puppy
Subject description: remastering Lupu 520
 

G'day emil,

I must congratulate you again for your efforts with R - much appreciated, thank you! Like hayden I've also had problems remastering Lupu520 into a straightforward "R-pup" using your pets and listed dependencies (i.e,. tcklt, gofortran, lupu_devx_520 etc). Mind you, I've never had any luck burning copies of my operational puppy from hard-drive to CD - I must be missing something obvious although I follow the help dialogues to the letter.
I can produce the LUPU 520 ISO with all your extra pets on the CD so that they can be regenerated 'on the fly' for any fresh install, as I think you suggested in your previous post, but like hayden I think that might frustrate a novice user. I'm attempting now to remaster the LUPU 520 iso by swapping my operational (R- and Rcmdr-loaded) lupu.sfs with that generated from the 'Puppy live-CD remaster'. Again, I must be missing something really basic,

Cheers.

EDIT: Barking up the wrong tree again - obvious that only the current LIVE-CD is offered for remastering in the standard selections offered in Lupu 520, you have to go 'behind the scenes' to do a functional remaster as illustrated here by stu90/snuffer66 http://www.youtube.com/watch?v=i5xXWtkvw50 or the indomitable sneekylinux here http://www.youtube.com/watch?v=yQIqwy7_trs&feature=related and he has a Part2 linked with it also. Dougals ENHANCED remaster script is buried here http://www.murga-linux.com/puppy//viewtopic.php?p=282713&sid=2b61daccc6dd128a8d53847e2ad5850c and I'm just about to try it out now.

EDIT EDIT: Barking up another wrong tree - for Lupu520 shinobar has come to the rescue in cases of some sort of 'reused' SFS issue with a another updated RemasterPup2 here: http://www.murga-linux.com/puppy/viewtopic.php?p=485172&sid=4597c1bd714a341215f731a701c0932b, and pa_mcclamrock posted his Remasterpup3 here http://www.murga-linux.com/puppy/viewtopic.php?p=485172&sid=4597c1bd714a341215f731a701c0932b, which I'm about to try. Or cry trying.

OK those who've actually read through the reams of help threads are aware that there are 2 basic ways to remaster your own puppy - during a 'live' session in which you boot from a fresh base (with puppy pfix=ram), download and install all your preferred goodies (Pets and SFS's, browser add-ons, bookmarks etc), and then choose the 'Puppy Remaster Live-CD' route to personalise your distro. or;
INSTALL your fresh base to HDD or USB etc - creating a pupsav file in the rebooting process - and download and install all your preferred goodies (Pets and SFS's, browser add-ons, bookmarks etc as previous example. Correct me if I'm wrong somebody - not important whether you are running from a "Full" or "Frugal" install.) This secondary route doesn't appear to come standard in the official Puppy5's, from what I have seen.

I note similar disappearances and 'ghosting' as hayden described for emil's R- and RCommander pets after rebooting, undoubtedly related to the /mnt/home installation path noted earlier in this thread as an issue on Monday 3rd Jan. The respective file lists in ./packages are stripped (i.e., "R-2.12.1-i486.files" and "Rcmdr-2.12.1-i486.files") and as everything else appeared intact I thought if I just repaired and preserved those files by changing the Permission rights on them, they would not be corrected on reboot. Don't try that solution, folks - that leads to kernel-panic City.

I'll try emil's workaround - maybe I'll understand it when I try it - I think you mean remastering via the hdd-install route rather than the live-cd route, emil? I wonder whether you'd care to re-compile the pets to install in the expected manner, or perhaps post an SFS combining those pets - some stage in the future? Many thanks for all your work to date, emil.

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emil

Joined: 10 Nov 2009
Posts: 616
Location: Austria

PostPosted: Tue 18 Jan 2011, 15:24    Post subject: remaster  

Hi puppyt - greetings and best wishes to Australia and especially to the regions and victims which were hit by the flooding.

I see 2 distinct issues:

1) The fact that I compiled R to /mnt/home was motivated by saving place in savefiles. It grew quite popular recently (see open offce pets). From the responce so far it would had been better to make them at a place inside the "/" tree which is included into the remaster. Maybe I have a quick go at that.

2) I feel there is quite a deal of confusion in the conception of "remaster". I exclusively use a "manual remaster" procedure, which works fine for me. It is also much easier to understand and control what happens. Burning lots of dysfunctional CD'S makes no sense. Is there any interest if I write sort of a "HOWTO manual remaster"?

kind regards
emil

PS: try my new lithe version of my sage pupplet. (400 MB) there you can install Rcmdr and do a remaster, this should work fine. It is called sagelithe
http://www.murga-linux.com/puppy/viewtopic.php?p=487712#487712
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