Math Base - Basic Free Mathematic Software for Puppy Linux

Mathematical tools, physics simulators, CAD, CNC, etc.
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emil
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Math Base - Basic Free Mathematic Software for Puppy Linux

#1 Post by emil »

Hello math-lovers,

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Over the last weeks I have spent some time to get Basic Mathematic Packages working in Puppy Linux 431.

Those are:
GNU OCTAVE - For engineering and numerics (strong side matrix calculations). Mostly compatible to Matlab.
GNU R - standard package for statistics
MAXIMA - Computer Algebra System, also with GUI Frontend wxmaxima (similar to Mathematica and Maple)
GNU GRETL - econometrics and time series analysis
GEOGEBRA - interactive educational math package (high school level)
YACAS - tiny and efficient Computer Algebra
Sage - Huge, comprehsive and (all?)mighty package
NumPy, SciPy, SymPy - Python math modules
SciLab - Numeric package, similar to Matlab but not as compatible than Octave

the pet files also include amongs others gnuplot, GNU Lisp (glc), GNU Fortran (gfortran), GNU scientific Library and LAPACK libraries.

Beside beeing strong command line interpreters, most of these packages can be used as scripting languages.
I have packed the necessary pet files into tarballs.

Old Download links are not working any more, I have moved most packages to

DOWNLOAD
http://boxen.math.washington.edu/home/e ... are/Puppy4


Download Sage
at official Sage mirrors (choose your mirror, Linux binaries, 32 bit)

Scilab
forum member Q5sys postet this link: http://lhpup.org/team/Q5sys/scilab-5.2.2.sfs and this md5sum: http://lhpup.org/team/Q5sys/scilab-5.2.2.sfs-md5.txt

File List MathBasePup431.tar (Octave, R, Maxima):
gcl-2.6.7-i486.pet - Lisp (needed for Maxima)
gfortran-4.2.2.pet - Fortran (needed for Octave and R)
glpk-4.10-i486.pet - Numeric package needed for Octave
gnuplot-4.2.5-i486.pet - gnuplot for graphics of Octave and maxima (command line)
libiconv-2.5.0.pet - R needs the library and symlinks
maxima-5.2.0-i486.pet - CAS
octave-3.2.3-i486.pet - Numerics
R-2.10.1-i686.pet - Statistics
wxGTK-2.8.9-unicode.pet - GTK for the wxMaxima frontend, custoz to disciple
wxMaxima-0.8.2-i386.pet - Maxima GUI, courtesy disciple

File list gretl_for_puppy:
fftw-3.3.3.pet (Fast Fourier transform)
gfortran-4.2.2pet (fortran compiler - same as in octave package)
gnuplot-4.2.5-i486.pet (gnuplot - same as in octave package)
gsl-1.13-i486.pet - (GNU scientific library)
lapack-3.2.1-i686.pet -(Linear Algebra Package)
libxml2-2.7.2-i486.pet - (XML Library)

File list for Python modules
gfortran-4.2.2.pet
gnuplot-4.2.5-i486.pet
gnuplot-py-1.8-i686.pet
ipython-0.1.0-i686.pet
numpy-1.4.0-i686.pet
python-2.6.4-i386.pet
scipy-0.7.1-i686.pet
sympy-0.6.6-i686.pet


Yacas is a single pet and Geogebra is a Java Package (need Java installed), sage is packaged to an sfs

How to install
Unpack the tarballs and install all pets (Or just those you need).
Geogebra: install Java, more Information GeoGebra Threat
Sage: install sfs files (see this thread page 2 for details)

How to run
Open a console and type octave, R, maxima, gretl, yacas, sage, ipython (case sensitive).
wxmaxima can be run from Menu/Utility
To run Geogebra unzip it and run the script geogebra.sh in its base directory.
For R there are also 2 GUI's (PMG and Rcmdr) working, more info at the R -thread

This software packages are powerful tools for education and studies. I like the idea that you can put it on a pendrive and use your Puppy at home and at school/university.

I think these are the basic free and open source Math packages (I didn't add scilab yet because it doesn't offer much more than octave, which in turn is more compatible to the Matlab, the industry standard).

Misc:
I must admit I am a new user, and probably those packages could be smaller. I have just skipped some documentation, since this is easily found on the net. I haven't tested the programs very much, feel free to notify me if there are problems.
I also tried to put everything together in a sfs File but failed (it is not working properly) maybe someone with a clue can do it if need arises.

I sincerly hope more people come up with science and math software for puppy linux!

Servus
emil

21.01.2010: edited to include gretl, yacas and geogebra
22.01.2010: edited to include sage
26.01.2010: edited the link to R GUI's PMG and Rcmdr
29.01.2010: edited to include Python packages
13.05.2010: edited to include Scilab package

---
5.474 The number of fundamental operations that are necessary depends solely on our notation. - Tractatus
my place
Last edited by emil on Thu 25 Nov 2010, 10:07, edited 11 times in total.

DMcCunney
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#2 Post by DMcCunney »

This is a nice attempt, but has issues.

FileHost.org wants you to provide an email address, and they email you a link to grab the file. I did so, but the tar.gz file I got was broken. I get an unexpected EOF error from tar trying to extract it.

I'm not sure whether the archive you uploaded was bad or it got garbled in transit. Attempts to re-download time out, as though the hosting site went off the air.

It doesn't appear possible to use the direct link in your post.
______
Dennis

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Dingo
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#3 Post by Dingo »

Woof Woof

I mirrored (and organized separately, with respective dependencies) math apps by emil, here:

http://puppylover.netsons.org/dokupuppy ... :math_apps

The goal of Dokupuppy is avoid vanishing of useful software, I have ever a copy of files on my local hard drive, if any file disappears (but I check from time in time in orderto avoid this) you can e-mail me at address on this dokupuppy front page

http://puppylover.netsons.org/dokupuppy
replace .co.cc with .info to get access to stuff I posted in forum
dropbox 2GB free
OpenOffice for Puppy Linux

emil
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Broken files?

#4 Post by emil »

Hello,

@DMcCunney: Thank you for testing, you are probably right.

@dingo: Thank you for the mirror - Did you experience any problems with the download?

I tested the original link and must admit I also had problems with the download. So I removed the file (maybe to quick?), before I saw dingos post.

I uploaded again with a new link
http://www.filehosting.org/file/details ... Pup431.tar

I will also edit the original post and provide a md5 checksum.

dingo, could you please also correct the link in the mirror, sorry for the hazzle.

Most of this files were already available on this forum, only maxima and lisp are new. If the problem with the large file persists I can post those seperatly. (I will not be online the next few days, so please be patient).

Maybe I have still time to check if dingos links are working.
All the best
emil

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Dingo
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#5 Post by Dingo »

I downloaded from original link you have posted, without any pain anyway next days I'll add another mirror also meantime I'll update links for all-in-one-tar.gz package
replace .co.cc with .info to get access to stuff I posted in forum
dropbox 2GB free
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charlie6
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#6 Post by charlie6 »

Hi emil,
many thanks for this !
Just wanted to know if this package could run on puppies (4.1.2; 4.20...) with k.2.6.25.16 or older kernels?
Thanks for your answer
Cheers, Charlie

emil
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older kernals

#7 Post by emil »

Hi charly

To be honest, I haven't tried. I just have puppy 4.31 running.
Could anybody try and tell us if it works?
emil

disciple
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#8 Post by disciple »

The R package (and dependencies) runs on Puppy 2.16 (k2.6.18.1). I haven't downloaded the others, but I think it is extremely likely that they will work... apart from things like kernel modules it is pretty rare for anything to care about the kernel version.

Thanks for these Emil, and for splitting them up Dingo. It is good to keep packages of libraries and separate programs separate, so people can also use them with other programs or newer versions, without downloading big things they don't need.

This is just what Puppy needed :)
Misc:
I must admit I am a new user, and probably those packages could be smaller.
Yes, there are a couple of basic things to keep in mind in future:
- before running dir2pet check that binaries and libraries are stripped (right-click on them in rox and look at the properties). e.g. the R binary was stripped, but the libraries weren't. You can run `strip --strip-unneeded /usr/local/lib/R/lib/libRblas.so /usr/local/lib/R/lib/libRlapack.so` to strip them.
- you can compress binaries with upx (search for it on the forum). This doesn't really make the .pet smaller (as it is compressed anyway), but it does make it take up less space when it is installed. Space in a save file is important in Puppy :)
Often a lot more space can be saved by deleting other stuff that isn't usually needed, but that takes a bit more time and knowledge about what you are packaging.
There is also a forum thread somewhere about compilation options to make things smaller, but I've never spent the time to get into that stuff.
Do you know a good gtkdialog program? Please post a link here

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MinHundHettePerro
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Re: MathBase - Octave, R, Maxima

#9 Post by MinHundHettePerro »

emil wrote:Hello math-lovers,
...
GNU OCTAVE - For engineering and numerics (strong side matrix calculations). Mostly compatible to Matlab.
...
Just downloaded, if this means I can run Matlab-scripts in puppy (without installing the Linux version of MatLab, which is Huge) it'd make me a very happy puppy user :) . If not, I would probably be happy anyway (re-writing, adapting :( :)) :). Have used Gnuplot before (long ago and in a cygwin environment, though) and found it rather versatile 8).
Will install and try it out within the week (to much work at the mo. :() :) .

Cheers :)/
MHHP
[color=green]Celeron 2.8 GHz, 1 GB, i82845, many ptns, modes 12, 13
Dual Xeon 3.2 GHz, 1 GB, nvidia quadro nvs 285[/color]
Slackos & 214X, ... and Q6xx
[color=darkred]Nämen, vaf....[/color] [color=green]ln -s /dev/null MHHP[/color]

disciple
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#10 Post by disciple »

Just to help people get started, after installing R and its dependencies I:
- ran

Code: Select all

R

- added a couple of numbers together to check that it was working
- ran

Code: Select all

help(chooseCRANmirror)
(because I read the manual about how to install packages)
N.B. you can get a general help just by running help(), and when you are in a help you can get help on using the help() by pressing h. And you exit a help by pressing q.
- ran

Code: Select all

chooseCRANmirror(graphics=false)
because chooseCRANmirror otherwise wanted to use a dialogue, but I don't have tcl/tk installed, and if there is an xlib gui I don't know how to tell it to use it.
- ran

Code: Select all

chooseCRANmirror(graphics=false)
and told it the number of the mirror I wanted to use.
- ran

Code: Select all

install.packages("s20x")
to install the s20x library. I have the devx, but I don't think it did any compiling or anything, so it would be good if someone without the devx could try installing a package and report back. I imagine some packages would require compiling, but not others. I think all it did was create /usr/local/lib/R/library/s20x, so I have made a .pet of that; please report if it works.

I imagine there is lots of information on the internet about using R... the trouble is finding it, since it has such a useless name :)!

BTW you exit R with

Code: Select all

quit()
Last edited by disciple on Tue 12 Jan 2010, 12:02, edited 1 time in total.
Do you know a good gtkdialog program? Please post a link here

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disciple
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#11 Post by disciple »

They like to use s20x in engineering maths classes.
You need to load libraries like this:

Code: Select all

library(s20x)
I think you can check if what is in my .pet is all that is needed to install s20x just by trying to run an s20x command - say

Code: Select all

interactionPlots()
, even though that just produces an error message because you didn't provide the right input arguments.

N.B. for some reason the file paths in /root/.packages/s20x.files are showing up missing the y in library for me... does anyone know why that is? Seems like a bug in petget.[/code]
Attachments
s20x.pet
(162.77 KiB) Downloaded 1791 times
Do you know a good gtkdialog program? Please post a link here

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emil
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Getting startet

#12 Post by emil »

Hello math-lovers,

I am glad that the packages seem to work and you like them.
I thought I add some links to get startet.

OCTAVE Homepage - Packages - Tutorial try also Matlab Tutorials and Examples
R Homepage with tons of Links Edit: http://rseek.org/ thanks @ carolus
MAXIMA Homepage - Tutorial - Wiki

@disciple
thanks for testing the older kernel and also your advice on pet stripping. Do you think compile options --enable static --disable shared would help? I read something about those options but cant remember where.
Thank you also on the short intro to R and your link to the s20x library.
Why do you think R is a useless name for a programing language? Just as compared to e.g. C :D ???

@MinHundHettePerro OCTAVE/MATLAB Compatibility
Good news is that for basic work and scripts Octave will run Matlab scripts fine without changes, or they will only need really minor tweaking. In my "main" side-project I try to get a Chemical package running (CANTERA, C++) which has Library Wrappers for Matlab and Fortran. I changed the source to use Octave instead of Matlab. Most demos and examples of this package run without change, I just have problems with a few who use Matlabs implementation of Class-Inheritance (which is still a rather exotic feature). Advanced features (e.g. specialised functions, GUI Interfaces) will need more work and patience if you intend to port them.

Some Links on this topic:
Octave <-> Matlab Compatibility Database
Wiki
Homepage FAQ

Geany is a perfect little IDE for Octave scripting. You can set the proper format in the Menu Document->Set Filetype->Scripting Langugage. It will autodetect the format for all .m file extensions.
I use Menu Build->Set Includes and Arguments Compile:<blank> Execute: octave -q --traditional "%f"
the option -traditional will help with Matlab compatibiliy.
And of course put this in
Menu Edit->Preferences->Tools: /usr/bin/xterm -e bash -c

Ok, have fun, Christmas/Newyear time is over, back to some serious work.
emil
Last edited by emil on Wed 20 Jan 2010, 19:06, edited 2 times in total.

disciple
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#13 Post by disciple »

Why do you think R is a useless name for a programing language? Just as compared to e.g. C
Yes, it is even harder to find information on C, as I can't search for "r statistics" or add "CRAN" to the search
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carolus
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#14 Post by carolus »

disciple wrote: I imagine there is lots of information on the internet about using R... the trouble is finding it, since it has such a useless name :)!
Supposedly the following search engine gets around that problem, but I haven't tried it:

http://rseek.org/

disciple
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#15 Post by disciple »

Great! Thanks for that.
Do you know a good gtkdialog program? Please post a link here

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Minimatter
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about R

#16 Post by Minimatter »

disciple,

Since you ask where the name "R" came from, here is a little history. Starting in the mid 1970's, statisticians at Bell Laboratories developed a new language interpreter which they called "S" to tie together statistical calculation routines, mostly in Fortran. It is one of the earlier large programs written in "C", which the people down the hall were developing along with the UNIX operating system at the time. I understand "C" itself is so called because its predecessor was "B". By the mid 1990's, a commercial version called S-PLUS held a large market share for statistical software (rivalling SAS). It is still sold.

R was developed starting about 1997 (by two professors in New Zealand) as a free alternative, reimplementing the S language with new code. As for the name, it is clearly a takeoff on "S". Remember the computer HAL in Kubrick's 2001? Also, the first names of the two professors are Robert and Ross. True, it is not a good name for searching on. R is at this time arguably the dominant statistical calculation system in use; its maintainers are the top people in the statistical computing field. The best source of information on it is its home page www.r-project.org.

Emil, thank you for providing newer versions of R and Octave for the community. Another you might go after is the econometrics and time series program gretl. To date, I've been using precompiled versions (for Red Hat EL4) which the home sites for R and gretl provide.

Minimatter

disciple
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#17 Post by disciple »

Since you ask where the name "R" came from
You're putting words in my mouth ;) I was familiar with most of that :)
The best source of information on it is its home page www.r-project.org
Yes, I didn't think it was that great for finding tutorials and examples, particularly involving different extensions, but it's a while since I looked, and maybe I missed something... like maybe the R reference index :)
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Re: MathBase - Octave, R, Maxima

#18 Post by Puppyt »

emil wrote:Hello math-lovers,

Over the last weeks I have spent some time to get Basic Mathematic Packages working in Puppy Linux 431...

GNU R - standard package for statistics...

the pet files also include gnuplot, GNU Lisp (glc) and GNU Fortran (gfortran)...
EMIL YOU BLOODY RIPPER !!!

That's my immediate response in my mother tongue that, when translated to everyday English means that you are to be celebrated and held in awe for your efforts and abilities beyond those of us mere mortals. I've been waiting ages for an update on the R package for Puppy, and you've picked up from where cb88 (and his "Mathpup") and debernadis (and his redoubtable "Rudypuppy") left off. THANK YOU!

Now I've confessed my linux-illiteracy I also confess my statistical ineptitude - do you have any tips on running Rcmdr (R Commander - a GUI for statistical and R newbies) from within Puppy? I was using R and Rcmdr under wine or trying the deb version under gposil's dpup477 (retro version), but it will be a few weeks before I can try your R pet and download Rcmdr under the CRAN repositories for myself - I wonder whether the installation of such R packages from within standard (non-dpup) Puppy might encounter problems.
Bugger it - downloading now into dpup, I'll give it a go myself...

Meantimes Dingo, many thanks indeed for your Aladdin's Cave of resources at Dokupuppy. Has been incredibly useful to me in the past - only place to find sketchman's original CUpup, for example - your mirror is most appreciated.
In R's case, I hope that it makes it into the official Puppy repositories.

Cheers!

emil
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Response and some notes on the compile process

#19 Post by emil »

Hello,

@Minimatter
I must hold myself back from doing gretl (actually I had already downloaded the source). There seem to be some dependencies and I have to refocus my time schedule.
@disciple
In my opinion it is highly remarkable, that for 2 letters out of 26 (C, R) the nr 1. find in google are programming languages (7.7 %) :D. - It has become a tower of Babel imho.
@ carolus
Thank you for this great http://rseek.org/ link !
@ Puppyt
I am happy about the enthusiastic response ;) BUT

actually my abbilities are not that impressive. Puppy Linux is my first real POSIX experience (a very pleasent one, that for sure). What really IS impressive is that I could build those programs and that I had fun doing it!
you've picked up from where cb88 (and his "Mathpup") ... left off.
I found the Mathpup - thread when I searched for a usable octave. pet. I must admit the negative aftertone of this threat was my sole inspiration to compile R and Maxima. This thread still comes up top when you google for Puppy Linux Mathematic. Just to defend Puppy Linux from a math-deficit repute.

In contrary: In the course of posting this I googled out that the SAGE Project (big comprehensive open source math project) used Puppy Linux as technology platform (for live CD and SAGE on Windows/Mac in a Virtual Box). They changed to a minimal Ubuntu though in the meantime.

About documentation and learning
Those packages are mighty tools, not solutions. The software-technical-aspect is in most cases the easier side of problems (sorry, no 'kings way' to the math). Best approach is learning by doing, i.e. use the software for actual problem-solving. Above the average level of tinkering and googling and a steep learning curve is to be expected. That said, if anyone finds a particular helpful tutorial for beginners post a link here. Everything advanced should go to the specialist forums or mailing lists.

About compiling:
I really encourage everyone to compile from source. it is not that big a problem, most of the time. I found that in many cases it is even faster than googling lots for existing packages. To often you will end up with old packages which are not working. Finding the right mix between compiling and googling is the key. After installing the devx.svs it is basically 3 steps:
  • download and unzip source
    read readme/install files
    follow the instructions
In most cases it will be as simple as ./configure, make, new2dir make install to get a pet. With the exception of Octave all those packages were easy to build. Most important are the GNU compilers of the languages, great work those guys are doing! Math packages use similar stuff (fortran, Blas, gnuplot, Lisp), so step by step adding additional packages becomes easier because you already have those installed.

Octave: The configure process gave lots of warnings. The only package I added was glpk. All other warnings I ignored (in the end, because after much tinkering I couldnt get rid of them).
Warning: I tried to use optimized BLAS, but it was a big waste of time, because Atlas-package is machine dependent and a real time eater (it compiles the library over and over with different compiler settings, benchmarks them and then chooses the best settings).
Possible improvements: I couldnt get gotoblas, which is machine independent. I also failed to link FFTW (fourier transform) and Metis (sparse matrix) packages, but those are needed for cutting edge speed. For the graphics I sticked to gnuplot, there are other alternatives but what I learned from the octave forums gnuplot is a good choice.

Maxima: get Lisp (glc) first, then ./configure, make, install - and then add disciples wxmaxima pets.
R: was just ./configure, make, install on my full install (I was stunned - but on the other hand: this is really a well tended plant in the garden of free code!). On my frugal test install I had to add the libiconv.lib, but that was all.

So it should be no problem to recompile if new versions appear.

Future projects
As mentioned I have to cut back on this math stuff but If I find time I would be interested to see GEOGEBRA work (Excellent tool for classroom maths, but in Java). It should work out of the box with installing Java in your puppy but more interesting would be to compile the package with GJC ...
I had already a go on YACAS, this is really small (puppy size) and - just an idea - replace some of the numerous calculators with this tiny CAS in future puppy releases?

It would be a privilege to but those packages in the official repositories, but I think somebody more experienced should have a closer look (to trim the fat and maybe put those into a .sfs file alternativly)

all the best
emil
Last edited by emil on Wed 20 Jan 2010, 10:11, edited 1 time in total.

emil
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YACAS

#20 Post by emil »

Hello,

I tried Yacas, which sounds very interesting beeing such small size.
But this thread is rather dated and the pet doesn't work in my puppy 431.

So I recompiled and its working, even below 1MB.

Download it at:
download link

I have an issue that del-key is not working as expected. Do you also get this?

regards
emil

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