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 Forum index » Advanced Topics » Additional Software (PETs, n' stuff) » Engineering/Science/Simulation
The R Project for Statistical Computing
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aldir69

Joined: 12 Aug 2014
Posts: 6
Location: Lisbon, Portugal

PostPosted: Thu 14 Aug 2014, 15:17    Post_subject:  The R Project for Statistical Computing
Sub_title: R 3.1.1 SFS built with Puppy 4.3.1
 

Hi guys,

I've been compiling R from source for the last couple of years but this is my first attempt at creating a SFS.

It includes base R.3.1.1 plus a few extra packages, gfortran 4.2.2 and tcltk 8.5.6.

I didn't include JDK but it was compiled with JDK 1.6u27.

Here's the link to it Smile

http://1drv.ms/1mNLcNM

I'll be adding additional packages to it as time permits.

PS. I just tested it in Lucid 528.005 and it's working fine.

Long live Puppy Wink

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Puppyt

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

PostPosted: Fri 15 Aug 2014, 22:27    Post_subject:  

Good On You aldir69!!
You're a Puppian after my own heart - and your first post? Many Thanks Smile
I am downloading your sfs as I write. I myself have used the official Ubuntu deb packages to install R 3.0.3 into pemasus Precise 3.8.3-upup. I also managed to get R-Commander 2.0-4 installed, and R-Studio was pretty painless - but I haven't had the guts/time to produce a SFS upgrade for the R Puppy threads.
Looking forward to testing your SFS on backwards-compatible Lucid, and 431, I understand?
Cheers!

PS Off-topic here, but what do you think of SOFA Statistics? http://www.sofastatistics.com/home.php. It seems to be broken with its call-up of wxversion, in the puppy environment Sad

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aldir69

Joined: 12 Aug 2014
Posts: 6
Location: Lisbon, Portugal

PostPosted: Sat 16 Aug 2014, 07:57    Post_subject:  

Hi Puppyt Smile

I just wanted to give something back to the Puppy community, it's been so fun working with Puppy Linux the last few years, it's the first Linux I kept for more than a couple of months.

All the work from compiling to sfs building was done from my ThinkPad R30 running old trustworthy 431.

My main machine is a DELL Precision 470 and it's primary OS is Lucid 528, so I tested it there also.

Yesterday I managed to add JGR and Deducer to my R build, now I'm trying to incorporate JDK to my sfs.

Regarding SOFA, I just watched the videos, it has a good look to it.
But I'm old school and still prefer to be able to script my work, for reproducibility purposes. Wink

Also, my time is limited, so I have to focus on software that can be used at work. And I already have to deal with SAS and R (and Revolution R) and ... Sad

Cheers
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Puppyt

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

PostPosted: Sat 16 Aug 2014, 09:14    Post_subject:  

Feedback! Your SFS worked OOTB in Tahrpup 5.8.3, though I noticed that perhaps you hadn't included a menu entry (e.g., in "Business" category). I can get to 'R' fine via the terminal, so all good.
I then mucked around with installing the devx, before installing the latest stable R commander (with some jiggery-pokery with deb ODBC dependencies needed from PPM) and modified the Rprofile.site file to load Rcmdr automatically - so I have my spreadsheets and pulldowns without needing to learn the scripting (! to each his own Smile ) All seems to be working very well in that context, thank you!
Don't worry about SOFA and I appreciate you have more valuable things to do - I *finally* got it working, not in linux or in WINE, but going back to an old XP install I had. It's just not in the same market as R - I had wanted a quick'n'dirty interface for simple tests and data manipulation, but will hang onto my StatView for a bit longer for those functions, while I slowly develop proficiency in R.
Cheers!

PS Also using a ThinkPad - Lenovo T60

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aldir69

Joined: 12 Aug 2014
Posts: 6
Location: Lisbon, Portugal

PostPosted: Sat 16 Aug 2014, 12:22    Post_subject:  

Thank You for the feedback Puppyt Very Happy

I've been working a bit on this little holidays project Smile

My original idea was to build a complete R environment with all working OOTB with no extra dependencies apart from devx.

So next release will include:
- R 3.1.1 (with menu entry)
- JGR GUI (with menu entry)
- gfortran 4.2.2
- TCL/Tk 8.5.6
- JDK 1.6u27

Including JDK (and the additional packages) has almost tripled the file size to 207Mb, but it will be one less SFS to load.

I also added Deducer, just need to call it from inside JGR

Code:
library(Deducer)


Next time I'll see how to add it automatically to JGR.

Here goes the link to it

R-3.1.1_JGR_431_20140816.sfs
http://1drv.ms/1pp81fb

md5 = a6eeda074c5f91b2af6759d718715b3c


I'll be checking how to also add R commander Smile

Cheers
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step

Joined: 04 May 2012
Posts: 197

PostPosted: Sun 17 Aug 2014, 04:12    Post_subject:  

Thank you, aldir69! Is loading the devx sfs a prerequisite of your sfs?
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Puppyt

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

PostPosted: Sun 17 Aug 2014, 04:35    Post_subject:  

Sorry step - I think I might be confusing things. I needed to install the devx so that I could have R Commander automatically "make" and "compile" itself when I installed the "Rcmdr" package http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/. Then I could remove the devx.sfs for normal day-to-day use. I don't think you would need it for running the sfs' aldir69 is putting together - but I guess he will explain "...no extra dependencies apart from devx" in a later post.

EDIT: Hey aldir96 - so finally we might have an "R Puppy" in the kennel? Yippee - emil did some sterling work with his R /Rcmdr packages in the past (e.g., http://www.murga-linux.com/puppy/viewtopic.php?t=51141), but keeping up with all the Puppy versions (e.g., http://www.murga-linux.com/puppy/viewtopic.php?t=84013 and whatever GUI updates and dependencies would be a full time job Smile I am sure you'll pick a good "sweet spot" of kernel and R/R gui choices to last a goodly while, without having to worry about maintaining ad nauseum. Thanks again!

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aldir69

Joined: 12 Aug 2014
Posts: 6
Location: Lisbon, Portugal

PostPosted: Sun 17 Aug 2014, 08:16    Post_subject:  

Hi guys, thank you for the feedback Smile

step wrote:
Is loading the devx sfs a prerequisite of your sfs?


Not really, devx is only needed when installing or updating packages.

Puppyt wrote:
I don't think you would need it for running the sfs' aldir69 is putting together - but I guess he will explain "...no extra dependencies apart from devx" in a later post.


Here's the explanation Wink

What I do with R at home (in Puppy) is mainly R&D, so I'm always trying new packages. As such I always keep devx loaded.

Regarding R GUI/IDE, I think I will focus on the JGR/Deducer and R Commander/Plugins.

For me, RStudio is the best IDE available at the moment, and the one I use at work (and in my Lucid 528 box), but I won't try to put it in the sfs, to many dependencies for Puppy 431.

I'm curious to find out if this sfs works in other Puppy versions Embarassed
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Puppyt

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

PostPosted: Mon 18 Aug 2014, 07:38    Post_subject:  

Hi aldir69,
quick message to confirm your latest pet (R-3.1.1_JGR_431_20140816.sfs) works out of the box in both Tahrpup 5.8.3, and XP-like Hungarian - a Lupu 528-based puplet http://www.murga-linux.com/puppy/viewtopic.php?t=51144. No devx required. Thanks!

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aldir69

Joined: 12 Aug 2014
Posts: 6
Location: Lisbon, Portugal

PostPosted: Mon 18 Aug 2014, 11:14    Post_subject:  

Great news! Very Happy

Thank you Puppyt

Latest developments:

The sfs is going to grow a bit more, but I needed to include pandoc and the easiest way of doing that was to grab the binaries from RStudio and those are an extra 70Mb (sorry for that Embarassed ).

Now I can work on my rmarkdown files even without RStudio installed. Very Happy

Testing as I write.

Cheers
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step

Joined: 04 May 2012
Posts: 197

PostPosted: Sat 06 Sep 2014, 09:16    Post_subject:  

aldir69 wrote:

Latest developments:

The sfs is going to grow a bit more, but I needed to include pandoc and the easiest way of doing that was to grab the binaries from RStudio and those are an extra 70Mb (sorry for that Embarassed ).

Now I can work on my rmarkdown files even without RStudio installed. Very Happy

Testing as I write.

Cheers

Hi aldir69,

I'm testing R-3.1.1_JGR_431_20140816.sfs on FatDog64 700 alpha1. This is a 64-bit OS that loads a 32-bit compatibility sfs.
Both R and JGR start! R seems to work for most basic functions, however I'm having issues with library loading, which eventually boil down to iconv:
Code:

> install.package("xlsxjars")
...
* installing *source* package 'xlsxjars' ...
** package 'xlsxjars' successfully unpacked and MD5 sums checked
Error in iconv(x, "latin1", "ASCII") :
  unsupported conversion from 'latin1' to 'ASCII'
ERROR: installing package DESCRIPTION failed for package 'xlsxjars'
* removing '/opt/R-3.1.1/lib/R/library/xlsxjars'
...
> ?iconv
> iconv("testing","latin1","ASCII")
Error in iconv("testing", "latin1", "ASCII") :
  unsupported conversion from 'latin1' to 'ASCII'
>


The unsupported conversion from latin1 to ASCII is performed with iconv. I guess R includes its own iconv, as the OS 64-bit iconv binary is installed and working:
Code:

# echo testing | iconv -f latin1 -t ASCII
testing
#

I don't know what R is really looking for. This is what I can find:
Code:

# find /usr /opt -name '*iconv*'
/usr/share/man/man1/piconv.1
/usr/share/man/man3/iconv.3
/usr/share/man/man3/iconv_close.3
/usr/share/man/man3/iconv_open.3
/usr/share/aclocal/iconv.m4
/usr/share/glade3/pixmaps/hicolor/16x16/actions/widget-gtk-iconview.png
/usr/share/glade3/pixmaps/hicolor/22x22/actions/widget-gtk-iconview.png
/usr/share/gtk-2.0/demo/iconview.c
/usr/share/gtk-2.0/demo/iconview_edit.c
/usr/share/gtk-doc/html/pygtk/class-gtkiconview.html
/usr/share/slsh/iconv.sl
/usr/bin/piconv
/usr/bin/iconv
/usr/lib64/slang/v2/modules/iconv-module.so
/usr/lib64/siconv
/usr/include/c++/4.8.2/gnu/gcj/convert/Input_iconv.h
/usr/include/c++/4.8.2/gnu/gcj/convert/Output_iconv.h
/usr/include/gtk-2.0/gtk/gtkiconview.h
/usr/include/gtkmm-2.4/gtkmm/iconview.h
/usr/include/gtkmm-2.4/gtkmm/private/iconview_p.h
/usr/include/iconv.h
/usr/include/libgsf-1/gsf/gsf-output-iconv.h
/usr/sbin/iconvconfig
/opt/R-3.1.1/lib/R/library/utils/iconvlist
/opt/R-3.1.1/lib/R/include/R_ext/Riconv.h


aldir69, please take a look at this page
http://comments.gmane.org/gmane.comp.lang.r.devel/29712
it seems to imply the possibility that the binary you built isn't using the correct libiconv. I can't tell you much more, I know little about compiling, and I don't know if the 32-bit layer on my 64-bit OS can affect this issue.

Edit: I also tested the same sfs on FatDog64 631, the stable branch, but it fails due to a missing library, presumably required by the gfortran 4.2.2 package your sfs includes:
Code:

# R
/opt/R-3.1.1/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.2: cannot open shared object file: No such file or directory

So I will stick with FatDog 700 and try to fix the package issue.

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aldir69

Joined: 12 Aug 2014
Posts: 6
Location: Lisbon, Portugal

PostPosted: Sat 13 Sep 2014, 13:47    Post_subject:  

Thanks for feedback step.

With the return to work, the free time to play with Puppy has been very scarce, but I will look into it ASAP.

I agree with you, it might be a library version problem, it was compiled in PL 4.3.1.

I have to try with a newer PL release, but which one?
My main OS is still Lucid 528 Smile

Thanks again Smile
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step

Joined: 04 May 2012
Posts: 197

PostPosted: Sat 13 Sep 2014, 15:57    Post_subject:  

aldir69 wrote:
With the return to work, the free time to play with Puppy has been very scarce, but I will look into it ASAP.

I agree with you, it might be a library version problem, it was compiled in PL 4.3.1.

I have to try with a newer PL release, but which one?
My main OS is still Lucid 528 Smile

Thanks again Smile
Hi aldir69. Thanks for looking into this issue. Take your time, keep your job, it pays for the bills! I wish I could tell you which newer PL to compile on, but l haven't used Lucid much myself.
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