Puppy Linux Discussion Forum Forum Index Puppy Linux Discussion Forum
Puppy HOME page : puppylinux.com
"THE" alternative forum : puppylinux.info
 
 FAQFAQ   SearchSearch   MemberlistMemberlist   UsergroupsUsergroups   RegisterRegister 
 ProfileProfile   Log in to check your private messagesLog in to check your private messages   Log inLog in 

The time now is Sat 18 Nov 2017, 21:10
All times are UTC - 4
 Forum index » Advanced Topics » Additional Software (PETs, n' stuff) » Engineering/Science/Simulation
64-bit R Language and RStudio IDE - updated 2017-10-31
Post new topic   Reply to topic View previous topic :: View next topic
Page 1 of 2 [26 Posts]   Goto page: 1, 2 Next
Author Message
step

Joined: 04 May 2012
Posts: 950

PostPosted: Wed 08 Oct 2014, 15:20    Post subject:  64-bit R Language and RStudio IDE - updated 2017-10-31
Subject description: R 3.4.2 rstudio 1.1.383, built+packaged on Fatdog64-710
 

LATEST VERSION

R Project for Statistical Computing 3.4.2
RStudio 1.1.383 R IDE
R packages offered in SFS files are up-to-date 2017-08-31
Announcement and download/install istructions here: http://murga-linux.com/puppy/viewtopic.php?p=972877#972877.
These are 64-bit .txz packages compiled on and for Fatdog64-710. Pre-compiled R packages, including R commander, and SFS options for Fatdog64 and Puppy users are explained in the README file attached to the announcement post.

OLDER VERSIONS

R Project for Statistical Computing 3.4.1
RStudio 1.0.153 R IDE
Announcement and download/install istructions here: http://www.murga-linux.com/puppy/viewtopic.php?p=966091#966091.

R Project for Statistical Computing 3.4.1
RStudio 1.0.143 R IDE
Announcement and download/install istructions here: http://www.murga-linux.com/puppy/viewtopic.php?p=959577#959577.

R Project for Statistical Computing 3.4.0
Studio 1.0.143 R IDE
Announcement and download/install istructions here: http://www.murga-linux.com/puppy/viewtopic.php?p=954341#954341.

The R Project for Statistical Computing 3.3.3. Download/install instructions here: http://www.murga-linux.com/puppy/viewtopic.php?p=948152#948152.

RStudio 1.0.136 R IDE with markdown support. Download/install instructions here: http://www.murga-linux.com/puppy/viewtopic.php?p=938655#938655.

The R Project for Statistical Computing 3.3.2 and RStudio 1.0.136 powerful IDE for R with R markdown support. These are 64-bit .txz packages compiled on and for Fatdog64-710. Download/install instructions here: http://www.murga-linux.com/puppy/viewtopic.php?p=938655#938655.

The R Project for Statistical Computing 3.2.5 and RStudio 0.99.896 powerful IDE for R with R markdown support. These are 64-bit .txz packages compiled on and for Fatdog64-710. Download/install instructions here: http://www.murga-linux.com/puppy/viewtopic.php?p=903521#903521.
I add/update pre-built R binary packages silently, so visit the link from time to time to find out what's new.

The R Project for Statistical Computing 3.1.3 and RStudio 0.98.1103 IDE for R. 64-bit compiled on Fatdog64-700. Find txz slapt packages and sfs archives here: http://murga-linux.com/puppy/viewtopic.php?p=801845#801845.
along with an optional, all-in-one SFS of R binary packages.
I add/update R binary packages silently, so visit that link from time to time to find out what's new.

edits: 2017-10-31 R-3.4.2 rstudio-1.1.383 | 2017-07-03 R-3-4-1 | 2017-05-11 R-3.4.0 rstudio-1.0.143 | 2017-03 2017-03-18 R.3.3 | 2017-01-09 R 3.3.2, RStudio 1.0.136 | 2016-05-11 R 3.2.5, RStudio 0.99.896 | 2015-04-11 R 3.1.3, RStudio 0.98.1103, binary package SFS

_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus

Last edited by step on Tue 31 Oct 2017, 15:21; edited 11 times in total
Back to top
View user's profile Send private message 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Tue 02 Dec 2014, 16:23    Post subject: version 3.1.2 update and start R binary packages  

R 3.1.2 and some R binary packages. See first post.
_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Sat 11 Apr 2015, 16:43    Post subject:  

64 bit R 3.1.3 for statistical computing, RStudio IDE 0.98.1103 and 129 binary packages for R and RStudio. Packaged for Fatdog64-700 as txz and sfs. See links in first posting.
_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
greengeek


Joined: 20 Jul 2010
Posts: 4715
Location: Republic of Novo Zelande

PostPosted: Fri 08 Jan 2016, 15:02    Post subject:  

Thanks step - just downloading these for testing now. cheers!
Back to top
View user's profile Send private message 
greengeek


Joined: 20 Jul 2010
Posts: 4715
Location: Republic of Novo Zelande

PostPosted: Fri 08 Jan 2016, 15:58    Post subject:  

Hi step - I loaded the combined sfs and have a couple of questions:

1) I do not see any menu entry for R or RStudio. This is my first run with Fatdog64 - is there something else I should do after loading an sfs to get menu entries to show?

2) When I try to start R from a terminal I appear to be missing a lib needed to run. I have no savefile (I plan to run fresh from CD each time) so my libs are whatever comes standard with Fatdog64-701.iso
Can you suggest any package I can load to get hold of the appropriate libgfortran?
Code:
 /usr/lib64/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

cheers!
Back to top
View user's profile Send private message 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Fri 08 Jan 2016, 19:34    Post subject:  

greengeek wrote:

1) I do not see any menu entry for R or RStudio. This is my first run with Fatdog64 - is there something else I should do after loading an sfs to get menu entries to show?
That should be automatic in Fatdog64. When I load the SFS I do find new menu entries: R is under 'Calculate' and RStudio is under 'Development'. Perhaps you need to load the devx.sfs to enable menu category Development?
I load two SFS files:
R-3.1.3+rstudio-0.98.1103-x86_64-sfs.sfs
R-3.1.3-packages-x86_64-sfs.sfs
Quote:

2) When I try to start R from a terminal I appear to be missing a lib needed to run. I have no savefile (I plan to run fresh from CD each time) so my libs are whatever comes standard with Fatdog64-701.iso
Can you suggest any package I can load to get hold of the appropriate libgfortran?
Code:
 /usr/lib64/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
Definitely load the devx.sfs. I keep it loaded all the time. On a whim R can decide it needs to compile a new package from C or Fortran source, so you need the devx.
I admire your persistence!

_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Thu 12 May 2016, 10:29    Post subject: Announcing R-3.2.5 + rstudio 0.99.896  

The R Project for Statistical Computing 3.2.5 and rstudio 0.99.896, powerful IDE for R with R markdown support, are available for download from ibiblio.
Fatdog64-710 users should install directly from the gslapt package manager.

Pre-built binary R packages are available from my shared folder. I add/update packages silently, so visit the link from time to time to find out what's new. Having these packages is just a convenience; you can build all R packages from R itself.

Run-time R depends on the gcc and gfortran compilers, so you need to load the devx.sfs.

These packages include two ROX-apps and can install desktop icons and file associations. The installer scripts support keeping multiple side-by-side R and rstudio versions. So for future releases of these packages you will be able to try the new version without affecting an older version. Uninstalling the package from its ROX-app right-click menu is recommended.
rstudio-2.png
 Description   
 Filesize   97.15 KB
 Viewed   486 Time(s)

rstudio-2.png

rox-apps-2.png
 Description   
 Filesize   39.28 KB
 Viewed   477 Time(s)

rox-apps-2.png


_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
Puppyt

Joined: 09 May 2008
Posts: 756
Location: Gatton, Queensland

PostPosted: Sat 07 Jan 2017, 03:31    Post subject:  

Hi step- thanks very much for providing this, I installed your txz files for R-3.2.5 and rstudio-0.99 in my TahrPup64(6.0.5, devx on board) and was able to start a new project.
I ran into some problems though, which I think are systemic but not because this was compiled from a FatDog64/Slacko base. Firstly, I tried to install Rcmdr from the terminal in R, and then from within RStudio, and got the same result in several attempts. I think the main problem was that gfortran wasn't registered(?) or recognized properly from within the R environment, despite successful downloads from CRAN. I mucked about for ages today on this, and I guess that as a quick diagnostic you (dear reader) could check the output of an internal update from within R-Studio: Tools>Check for package updates>(select nmle)
Code:
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2  -c chol.f -o chol.o
make: gfortran: Command not found
make: *** [chol.o] Error 127
ERROR: compilation failed for package ‘nlme’
* removing ‘/usr/lib/R-3.2.5/library/nlme’
* restoring previous ‘/usr/lib/R-3.2.5/library/nlme’
Warning in install.packages :
  installation of package ‘nlme’ had non-zero exit status

...so I tried to install ggc-infrastructure.tar.xz from http://gfortran.meteodat.ch/download/x86_64/, but no change in the non-zero exit status of my install attempts. Do you (or anyone else) have similar issues in FatDog64 for such internal upgrades? step, could you consider including gfortran in your next update of your R packages? I'm probably making countless noob errors here, and will probably have to slink back to (learn) generating boxplots from the console, rather than a gui, in the interrim. Cheers Smile

_________________
What I get up to when I'm not on the Puppy Linux Murga forum:
http://scholar.google.com/citations?user=EMQxfgYAAAAJ
Back to top
View user's profile Send private message Visit poster's website 
Puppyt

Joined: 09 May 2008
Posts: 756
Location: Gatton, Queensland

PostPosted: Sun 08 Jan 2017, 04:35    Post subject:  

Hi step - could you shift the R packages from the '700' ibiblio repository over to the '710' directory please? Bit tricky using FatDog's gslapt package manager for a user new to the getup (*and* I had Broadcom-evil to deal with, for my wifi activation Smile) Finding out, yet again, that R+Puppy=no walk in park.
_________________
What I get up to when I'm not on the Puppy Linux Murga forum:
http://scholar.google.com/citations?user=EMQxfgYAAAAJ
Back to top
View user's profile Send private message Visit poster's website 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Sun 08 Jan 2017, 19:21    Post subject:  

Puppyt wrote:
Firstly, I tried to install Rcmdr from the terminal in R, and then from within RStudio, and got the same result in several attempts. I think the main problem was that gfortran wasn't registered(?) or recognized properly from within the R environment, despite successful downloads from CRAN.

The terminal log that you provided says "make: gfortran: Command not found". That's likely to be the root cause of your problems. You need the fortran compiler command installed - it isn't a library, it's a binary file plus a bunch of libs. It's part of the full gcc package. I checked devx_tahr64_6.0.5.sfs and it doesn't include gfortran. There isn't anything I can do about it, you'll have to either rebuild gcc fro Tahr64 with gfortran, or ask for gfortran in the Tahr64 support thread.

Quote:
.. despite successful downloads from CRAN.

When R on Linux downloads a package all it downloads is source code (not on Windows or OSX, just on Linux). Then R proceeds to compile the source code into a binary package. That's when it needs gcc and/or gfortran to be pre-installed in the system. Most packages just need gcc, but there are quite a few, especially the more common ones, that do need gfortran. So if you want to make significant progress with R you should get yourself gfortran.

Quote:
Do you (or anyone else) have similar issues in FatDog64 for such internal upgrades?

Not me, because I use Fatdog64 and its devx includes gfortran.

Quote:
step, could you consider including gfortran in your next update of your R packages?

Unfortunately, gfortran and its friend gcc are complicated packages that tie into lots of OS libraries, and they can be finicky. You really want to get them from the platform devx, not from me. Having said that, as a temporary patch, you could try a gcc+gfortran compiler package that I built for an earlier Fatdog64 release. But I make no guarantees and will not support it. Before you do, backup your savefile, because this is a package, not an sfs.
Here's the relevant info section from my "+Packages" post (in my sig)

step's post wrote:

gcc+gfortran 4.9.1: https://www.dropbox.com/s/2ppc70n9tfu7z39/gcc-gfortran-4.9.1-x86_64-1.txz?dl=1
On my hardware (Core2 Duo) the default fortran compilers that are included in Fatdog64 700 beta devx SFS builds crash (versions 4.8.2 and 4.8.3). This impacts both building R from sources and installing some R packages from the R prompt. So I built this newer gfortran version 4.9.1 to be able to build R 3.1.x. You should need gfortran 4.9.1 only if the default fortran compilers 4.8.x crash on your hardware too when installing some R packages. gfortran 4.9.1 is installed in /usr/local, so it can co-exists with the default GCC 4.8.x compilers. This package includes both and only gcc (C language) and gfortran compilers - they can't be separated, as far as I can tell.

I guess you could make an sfs out of this txz. Unpack it into a temporary folder, then run dir2sfs with the folder as input. Edit: mmm, Tahr64 doesn't appear to have dir2sfs,... search the forum for ways to turn a directory into an sfs, there are several choices

Quote:
... will probably have to slink back to (learn) generating boxplots from the console, rather than a gui, in the interrim. Cheers Smile

The boxplot commands are the same in the R console and in rstudio. But Rstudio is a joy to use in many ways. Try it.

Puppyt in his next post wrote:
Could you shift the R packages from the '700' ibiblio repository over to the '710' directory please?

I'm actually in the process of building the latest R, RStudio and collection of packages. I will announce to this thread soon. Stay tuned! I think I will include Rcmdr in the collection, so you won't need to worry about not having fortran - at least for that case.

Quote:
Finding out, yet again, that R+Puppy=no walk in park.
Smile
You'll soon see the sunshine again, I hope.

_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Mon 09 Jan 2017, 03:18    Post subject:  

@Puppyt, I sent you a PM.
_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Mon 09 Jan 2017, 11:22    Post subject: Announcing R-3.3.2 + rstudio 1.0.136  

The R Project for Statistical Computing 3.3.2 and rstudio 1.0.136, powerful IDE for R with R markdown support, are available for download from ibiblio.

Fatdog64-710 users should install directly from the gslapt package manager.
Other Puppy users please read the README file.

All users' README https://drive.google.com/open?id=0B932fvbgcXnMZnNUTEwxN2VmSjQ.

SFS packages and a collection of pre-compiled R packages can be found in my shared folder https://drive.google.com/open?id=0B932fvbgcXnMOW1TSDhyN0N4ajA.

I update the pre-compiled R package collection silently, so visit the link from time to time to find out what's new. Having these packages is just a convenience; you can build all R packages from R itself, provided that you have working C++ and fortran compilers installed. You need to load the devx.sfs and check that the gcc and gfortran commands are available (they are in Fatdog64).

These packages include two ROX-apps and can install desktop icons and file associations. The installer scripts support keeping multiple side-by-side R and rstudio versions. So you should be able to try a new version without affecting an older version. Uninstalling the package from its ROX-app right-click menu is recommended. The README file points out specific install/uninstall instructions for Puppy users. Fatdog64 users don't need to worry.
R-3.3.2-8r.png
 Description   Rstudio IDE
 Filesize   130.67 KB
 Viewed   277 Time(s)

R-3.3.2-8r.png

R-3.3.2-4.png
 Description   R commander
 Filesize   32.65 KB
 Viewed   271 Time(s)

R-3.3.2-4.png

R-3.3.2-3.png
 Description   R console
 Filesize   68.71 KB
 Viewed   277 Time(s)

R-3.3.2-3.png


_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
Puppyt

Joined: 09 May 2008
Posts: 756
Location: Gatton, Queensland

PostPosted: Thu 12 Jan 2017, 21:15    Post subject:  

Hi step - firstly a huge thanks to you for updating the R+Rstudio packages, Cheers! Have just PM'd you back after getting back from hols. I had RCommander working in a pristine copy of FatDog64-710, installed from within your R package, to get my boxplots. Unfortunately, I couldn't get Rstudio working even with the devx loaded. Getting back from the hols I find that I had "FatDog can't find save file" issues - and I'm still working through those but waitdev=3 seems to be working. Regret long download times and other demands will slow any further feedback. Many Thanks also for the gfortran pet on your dropbox - will try that later for testing your R sfs in TahrPup64/XeniaPup64. FatDogs' idiosyncrasies are not what I need at present. Thanks Again Smile

UPDATE: Using a new install of FatDog64-710, having loaded the devx sfs, R and Rstudio txz downloaded despite libjpeg dependency warnings (in devx, so no dramas?), then installed. 'R' works fine from the desktop icon, currently installing Rcmdr via terminal without problem - loads up fine with " library('Rcmdr')". However RStudio returns this error from terminal:
Code:
# rstudio
/usr/lib/rstudio-1.0.136/bin/rstudio: error while loading shared libraries: libgstreamer-0.10.so.0: cannot open shared object file: No such file or directory
#

I'm guessing I have an install order issue somehow, will shutdown and reboot, unistall and reinstall Rstudio etc etc to iron out this problem. Prolly just an uber-noob issue, on my side.

_________________
What I get up to when I'm not on the Puppy Linux Murga forum:
http://scholar.google.com/citations?user=EMQxfgYAAAAJ
Back to top
View user's profile Send private message Visit poster's website 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Fri 13 Jan 2017, 03:12    Post subject:  

Puppyt wrote:
Getting back from the hols. Thanks Again Smile
You're welcome. Hols sounds good!
So, yo sum up current progress::
- R and compiling R packages work for you in FD710
- rstudio doesn't work for you in FD710 yet, but you have savefile issues.
---> when you're ready, please open a terminal window and try these commands
which rstudio
rstudio
/usr/lib/rstudio-1.0.136/bin/rstudio
and paste results here, thank you.
- you plan on trying my PMed R sfs in in TahrPup64/XeniaPup64
---> Thank you, just remember that to compile with fortran you will need to get gfortran loaded/installed, either from the platform or from my compiler bundle, YMMV

_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
step

Joined: 04 May 2012
Posts: 950

PostPosted: Fri 13 Jan 2017, 03:27    Post subject:  

Puppyt wrote:

UPDATE: Using a new install of FatDog64-710, having loaded the devx sfs, R and Rstudio txz downloaded despite libjpeg dependency warnings (in devx, so no dramas?), then installed. 'R' works fine from the desktop icon, currently installing Rcmdr via terminal without problem - loads up fine with " library('Rcmdr')". However RStudio returns this error from terminal:
Code:
# rstudio
/usr/lib/rstudio-1.0.136/bin/rstudio: error while loading shared libraries: libgstreamer-0.10.so.0: cannot open shared object file: No such file or directory
#

I'm guessing I have an install order issue somehow, will shutdown and reboot, unistall and reinstall Rstudio etc etc to iron out this problem. Prolly just an uber-noob issue, on my side.


It should load those libs from /usr/lib64 and not /usr/lib

---> Do you have these files?
usr/lib64/libgstreamer-0.10.la
/usr/lib64/libgstreamer-0.10.so
/usr/lib64/libgstreamer-0.10.so.0

Are you loading the 32-bit sfs?
Did you change variable LD_LIBRARY_PATH?
---> open a terminal window and type
env
Do you see anything suspicious?

_________________
Fatdog64-710|+Packages|Kodi|Findnrun|+forum|gtkmenuplus
Back to top
View user's profile Send private message 
Display posts from previous:   Sort by:   
Page 1 of 2 [26 Posts]   Goto page: 1, 2 Next
Post new topic   Reply to topic View previous topic :: View next topic
 Forum index » Advanced Topics » Additional Software (PETs, n' stuff) » Engineering/Science/Simulation
Jump to:  

You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You can download files in this forum


Powered by phpBB © 2001, 2005 phpBB Group
[ Time: 0.0723s ][ Queries: 13 (0.0059s) ][ GZIP on ]