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Puppyt
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#61 Post by Puppyt »

:D
Thanks yet again, emil- as I have said before, you're a Legend.

I'll try that RKWard course you suggested, and thank you again for taking the time out again from your schedule for the Puppy "cause". I know that there has been a recent fracas elsewhere on the forum but I must say that you are a contributor who really represents the knowledge-sharing altruism that makes the Puppy Forum such a pleasure to visit.
I'll post back when I have progress, or readers can feel free to PM me.
Cheers!
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Xavi
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+1 to have rkward working for Puppy 5x

#62 Post by Xavi »

I'm working with a few research groups and teching institutions, and every now and then some professor wants to provide to LiveCD to his/her students with GNU/Linux, R and some easy-GUI-for-newbies (university students from Biology or similar, not-purely technical students).

We use R extensively for work, and RKward is an excellent compromise to use a good (a quite full-featured) mature GUI for R, much more that its java-based equivalents, or emacs+ess (too techie), or eclipse+statet (too big/hungry on hardware resources).

So +1 if someone is able to create some rkward for puppy 5x.
(sorry, myskills on puppy are still too low; hopefully one day I'll be able to help myself).

And why puppy 5x? Well, it seems that it comes with much more i18n features out of the box, and our users are from first courses at university, and not all of them are good in English, so it's a plus if they can have most puppy in localized languages + keyboards with just a few clicks from the puppy gui also, etc.

Thanks heaps puppy-devs for all your nice work!

(year after year, I'm impressed of the nice evolution of the puppy community.... )

Puppyt
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#63 Post by Puppyt »

G'day, Xavi -
thanks for your input, and welcome to the Kennels!
I've had to ask the broader Puppy community for advice on this point (here: http://www.murga-linux.com/puppy/viewtopic.php?t=67566), and although there appears to be great interest in terms of number of views, no solution just yet. This weekend I think I'll go back to LightHouse, now in version 5.03 http://www.murga-linux.com/puppy/viewto ... 956#499956. I've drifted away from LHP last couple of years to less "fully featured" Puppy derivatives, but tazoc and his team always bring a rock-solid base to the community so perhaps I should start afresh there. I'll keep you posted - I bet even Flan is still looking for progress on this point. G'day to emil too - a belated "thanks" for your input earlier regarding the RKWard Dilemma on that thread listed above -
Cheers :)
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emil
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#64 Post by emil »

Hi PuppyT and all,
I had a short try on the problem of Rkward after your last posts.
Compiling R with the shared library switch is no problem. But I couldn't get one of the KDE-packages to run on 511 properly. Lighthouse pup has a tested KDE package as far as I am informed, so I guess it could be good base.
emil

Puppyt
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#65 Post by Puppyt »

Thanks very much emil -
I downloaded LHP 503 (and Mariner SFS plus others) over a week ago for testing on this very matter. Over the weekend and during bootup from CD (puppy pfix=ram) on my main desktop it borked badly, and did likewise under VM VirtualBox - something about the GEForce videocard, I suspect. Perhaps also I encountered problems because LHP likes to set up a save file before first boot, whereas I much prefer not doing that until satisfied that the Puppy distro is a "keeper". (Particularly as my XP is needing a fresh install and major spring-clean/defrag of all its partitions.) Anyway I lost a bit of impetus but will try in a few hours on my Lenovo T60 lappie. I also downloaded John Biles' Legacy2.0 to experiment with as, although it is puppy2.14-based, I think it meets the criteria as far as pre-installed KDE (3.5.x) and java are concerned.
Thank you very much for running those tests on the Community's behalf, emil - there does seem to be a wide interest in adding RKWard to the R repertoire in Puppy. More in a few hours,
:)

UPDATE: 10 hours later, and I regret that I had problems on the T60 with both Legacy2 (which failed to complete booting from CD - all iso/cd integrity tests OK) and LHP 5.03. In the latter case I blame myself for poor preparation - LHP does things a little differently in terms of installation, and although I installed Mariner.SFS and also tried the LHP-repository's java pet (installed external to the main save file), emil's R+RCmdr lupu SFS installed but R kept dropping out. A quick test from the console revealed a problem with a shared library. There were also other strange bash issues (the only thing I know about bash involves my forehead and a brick wall) and the JRE manager appeared to 'forget' settings saved from the last shutdown. So I'll wipe that and arrange a frugal re-install, and if pain persists I'll email tazoc for some hints. LHP is a very different puppy to what I'm used to, but I like what I've seen (outside R) and will persevere.
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emil
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R for slacko

#66 Post by emil »

Updated first post for R sfs compiled in slacko RC

alas
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#67 Post by alas »

thank you very much for the update.

I have a question regarding R. I have tried to update the library in order to get packages that are provided for R 2.14 only (as f.ex. the tm package), but can not get the list updated. I think I am missing the dev package in order to do that. Is it possible to include it within your sfs, or should we wait for 2.14 for puppy? thanks a lot for your work!

alas

emil
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#68 Post by emil »

Hi,

I will not include the developement files in the R sfs. Usually every Puppy linux ships with a special "devx" sfs package which includes this tools. I don't know which puppy Linux version you use, but if we assume you use slacko you would have to download
http://distro.ibiblio.org/pub/linux/dis ... _5.3.1.sfs
Usually the creater of a puppy variant publishes a download link for the right devx sfs together with the iso file.

I am not the right source for details of the update process - I have never done this before. Maybe someone who have accomplished this can enlight us.
I also found this
http://stackoverflow.com/questions/1401 ... on-windows
but you probably know it already...

merry christmas :D
emil

alas
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#69 Post by alas »

thanks emil, indeed, I am running slacko and I have forgotten that I can use the devx sfs package for puppy slacko. I shall try that and report back.

I usually do (within R):

update.packages (lib.loc = "/usr/local/R/library/")

in order to update the libraries. This "should" enable to back port packages which are not available for R 2.13.2. Now, there are probably other ways, as f.ex. installing an older version of the needed packages. However, a newer one is always better. Thanks again for your work, and merry christmas to you.

alas

emil
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#70 Post by emil »

alas,

thinking twice you might also need to add gfortran which unfortunately is not included by default in puppies devx. (I would prefer it very much over other stuff like Vala or bacon which IMHO is not really used very much, but adds nothing to the compatibility or ability to compile lots of important software packages //Rant mode off - it's christmas :D )

So if you have problems updating R maybe also install gfortran beside devx (pet on this forum section should work, else use package manager).

cheers 8)

alas
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#71 Post by alas »

emil,

thanks again. I did install the devx file only, and I have updated R packages easily with update.packages() from within R.

Then, I have added missing packages manually (I have downloaded the last version of the packages from the cran archive, and I have installed their deps). After that, I can install missing packages from within R without issue.

Thanks again for your help on this, happy new year!

alas

emil
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R-2.14.1

#72 Post by emil »

I made very simple pet packages for the new Saluki Puppy:
R-2.14.1-i486.pet (18 MB)
R_DEV-2.14.1-i486.pet (88 K)
R_DOC-2.14.1-i486.pet (14 M)
R_NLS-2.14.1-i486.pet (733 K)
---
R-2.14.1-Saluki.sfs


Type was just ./configure, make, new2dir make install.
Start with Menu entry (Business) or from the commandline with R
As far as I know it should also work in Wary and Racy.
Please test :D
emil
Last edited by emil on Tue 24 Jan 2012, 23:58, edited 1 time in total.

Puppyt
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#73 Post by Puppyt »

Thanks emil :)
I want to get back to developing an "R-Puppy" over the coming months and these will be very helpful,
Cheers!
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alas
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#74 Post by alas »

thanks a lot for these new packages emil.

a R-puppy would be a very nice project... but as i am using emacs now, i am thinking about another thing: why not a kind of 'emacs-puppy' which would integrate everything -- like for instance R using EMS, and also org-mode (which is amazing by the way) -- on a quasi barbone puppy? The advantage would be to have a very light distro, a powerfull editor doing most of the job, and some external apps for the remaining tasks -- a kind of emacs-as-os on steroids? just thinking loud though...

all the best,

alas

emil
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#75 Post by emil »

I am a bit slow to reply these days.
Emacs puppy sounds good, but I think it should be easy to install in any puppy anyway. Emacs will always appeal to advanced users, and it is impossible to include all mods or add-ons, but maybe use the new bar-bone Saluki as a base for it?
All the best for your project
emil

pabloabc
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R and RStudio

#76 Post by pabloabc »

Hi to everybody!

Although I'm using several tastes of Puppy linux since long time ago, this is my first mail here...

First of all, congratulations to all the supporters and the people that is working hard for such a wonderful distro.
I'm very happy with it. Thanks to all of you.

Now my problem...

I'm using LxPup12.12 I think it is an Ubuntu 12.04 precise compatible Puppy with a light Graphical front, similar to Lubuntu.

Now, I'm starting a Coursera Course to learn R and RStudio so I need to install them in this Puppy linux machine.
That is mandatory for the Course.
At the moment I know almost nothing about neither program...
Only that they are statistical opensource programs.

My first attempt was to search, download and install Saluki's R-2.14.1-Saluki.sfs
Tha sfs was posted in the link below by emil on 2010 I think.
http://www.murga-linux.com/puppy/viewtopic.php?t=51141

Once the sfs is loaded as usual, I opened a terminal and typed R. The R promt came and the program was running smoothly.
Ran some demo library's packages and everything was ok with the R program in the terminal.
The second step was to install The RStudio. I couldn't find any pet for this so I decided to download
the .deb package and installed it with the provided pet instaler.

It created a menu entry but when I tried to run it, it says in a window :

R shared library (/usr/local/lib/R/lib/libR.so) not found. If this is a custom build of R, was it built with the --enable-R-shlib option?

After that the RStudio program exits.
Not sure what's wrong but for sure I don't know how to fix it... I've never built anything in puppy linux.

Anyone can find a simple solution to fix this annoying problem ? or
Maybe there are some properly pet/sfs packages to have RStudio running?

Also I want to know how do I uninstall the not runing .deb RStudio ?
The downloaded package was rstudio-0.98.501-i386.deb (32bits) ?

Sorry for my English. It is my second language...
Thanks a lot for your help.

emil
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#77 Post by emil »

Dear pabloabc,

The first thing which comes to my mind is to install R a via the included puppy package manager. If it is not available, than please look at the CRAN website for a package that fits to your puppy version.

Mixing different packages (like my compile for Saluki and a debian package for RStudio) is asking for troubles. I am sorry that it is impossible for me to give support for the multitude of puppies and variants in use.

Maybe this link is some help:

http://livesoncoffee.wordpress.com/2012 ... ntu-12-04/

If you want to use a Debian 7 compatible, puppy like base system, with apt-get package manager, for which you will likely find deb packages and instructions for most scientific software, then please consider to try

saintless et al, DebianDog:
http://murga-linux.com/puppy/viewtopic.php?t=93225

or even my CAT041:
http://boxen.math.washington.edu/home/e ... T-0.41.iso

cheers
emil

emil
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#78 Post by emil »

Dear pabloabc,
sorry my answer somehow didn't went through yesterday.

My first suggestion is to try to install R from the Ubuntu repos using the puppy package manager with your current puppy version.

then you could try to install the Rstudio binaries from their home page.

Mixing different versions, like my package for saluki and the ubuntu debs is asking for troubles.

I am sorry that I am not able to give detailed and tested help for every puppy version. My personal approach changed to favor Debian stable based versions like DebianDog or my CAT041. With those you have full apt-get and also in most cases you find detailed instructions somewhere on the web.

good luck and success,
emil

pabloabc
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#79 Post by pabloabc »

Hi emil and all !!

Thanks emil for your kind answer... It didn't solve my problem but guided
me to find the (not elegant ) solution at the moment.

To make rstudio run in LxPup 12.12 I downloaded the R package from an Ubuntu repository with the normal LxPup install tool and then i also downloaded the linux *.deb RStudio package taken from the RStudio site https://www.rstudio.com/ide/download/desktop

After instaling R it doesn't work at all. When I tried to run it, it said

/usr/lib/R/bin/exec/R: error while loading shared libraries: libblas.so.3gf: cannot open shared object file: No such file or directory

I searched for that file ( libblas.so.3gf ) in my computer and it existed there.

After a long time searching the web I could find some light here,
http://pebblesinthesand.wordpress.com/2 ... me-errors/

To fix R, I had to put the missing dynamic library path so R, could find it.
The command ldd /usr/lib/R/bin/exec/R confirmed that R couldn't find that library.

In a terminal, at the prompt, I wrote,
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/libbla

then again ldd /usr/lib/R/bin/exec/R confirmed that this time R sees every
dynamic library it needs.

At the prompt I put R and this time the program ran perfectly.

I exited the program R and in the same terminal that now have the path fixed, and I ran RStudio with the command /usr/lib/rstudio/bin/rstudio

Fortunately RStudio was running smoothly this time.

I know that this is not a definitive solution but it worked for me. Maybe someone who knows more than I can solve this issue in a more convenient manner.

Thanks to all for the help.

emil
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library paths

#80 Post by emil »

Hi pabloabc,

you could put the line

Code: Select all

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/libbla
into a configuration file like /etc/profile or alternativly maybe /root/.bashrc

so it is automatically added to the libary path when you start puppy.

Or maybe you could also create a symlink to the blas library (this is a very basic linar algebra library) somewhere in your existing library path (e.g. /usr/local/lib).

Thank you for your detailed report how you solved the problem!

kind regards
emil

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