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R language / Sciviews-K plugin
Posted by leoditolaghi
on 2009-10-22 12:53
OS: OS X Leopard
Hi all.
Can anyone tell me how to get Komodo Edit and the Sciviews-K extension working on Mac OS X Snow Leopard? I am running the 64-bit R interpreter, v. 2.9.2. The extension is installed, but I am getting an svMisc package error, and I think tcltk is not likely working. Does anyone have this extension working properly on Snow Leopard? I think it would be great to use.
Thanks for any assistance. R works fine on my system aside from this Komodo Edit extension challenge. I will probably opt to use Textmate if I can't get this running.
Thanks again,
Leo
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The following are some additional particulars:
# Environment:
# OS: Mac OS X 10.6.1 (Snow Leopard)
# R statistical software, Version 2.9.2
# (1) Setting Preferred R application to R tk
# (2) Executing Start R
# yields the following in the Komodo status bar:
# 'R --quiet --save GUI=tk' returned 1.
# ==================================================
# (1) Setting Preferred R application to R Terminal
# (2) Executing Start R
# yields (opening a blank tk window):
R version 2.9.2 (2009-08-24)
Error in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
'svMisc' is not a valid installed package
In addition: Warning message:
In fun(...) : Can't find a usable tk.tcl in the following directories:
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5 /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5/Resources/Scripts /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5 /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5/Resources/Scripts ./lib/tk8.5 ./lib/tk8.5/Resources/Scripts ~/Library/Tcl/tk8.5 ~/Library/Tcl/tk8.5/Resources/Scripts /Library/Tcl/tk8.5 /Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/tk8.5 /System/Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/8.5/tk8.5 /System/Library/Tcl/8.5/tk8.5/Resources/Scripts ~/Library/Frameworks/tk8.5 ~/Library/Frameworks/tk8.5/Resources/Scripts /Library/Frameworks/tk8.5 /Library/Frameworks/tk8.5/Resources/Scripts /System/Library/Frameworks/tk8.5 /System/Library/Frameworks/tk8.5/Resources/Scripts ./library
This probably means that tk wasn't installed properly.
# Also, presented with:
*** caught segfault ***
address 0x0, cause 'unknown'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
======================================================
Hi Leo,
Philippe Grosjean is the author of this extension. You may have better luck posting to the forum (or bug tracker) at:
https://r-forge.r-project.org/projects/sciviews/
Cheers,
Todd
Thanks, Todd
Cheers,
Leo
I am having a very similar problem with 64-bit R and Sciviews-K - I keep getting the "svMisc is not a valid installed package" error. Any luck with a solution?
I also posted to the scieviews R-forge page, as linked above.
Thanks,
Matt
I am getting a similar problem with R version 2.10.0 (2009-10-26), running on a Mac OSX leopard (i386-apple-darwin9.8.0)
Massimo
No. (Laughs)
Pulling my hair out, Matt (which is already in short supply).
Philippe Grosjean was very helpful, but it doesn't appear to be a Sciviews-K/Komodo extension problem. I am trying various R installations but no luck so far. Kinda takes the sheen off my newly-found Mac enthusiasm. I really hate the idea of running this under Fusion under Windows,as the SciViews-K extension looks like exactly what I wanted under an editor like Komodo.
Some rave about Textmate, though, which I have, but I haven't yet plowed that ground.
If I figure it out, I'll be sure to post it here (hopefully you'll beat me to it).
What's maddening is Philippe Grosjean's (who really tried to save me) comment:
"This is strange that the packages are compiled without errors, and then, that the software claims it is an invalid package. Moreover, I have reports that it works on R 64 bit." So some folks are cooking with gas, most likely.
Maybe a subtle Snow Leopard thingie?
Funny - I'm 100% with you regarding loss of a newly-found Mac enthusiasm.
Did Komodo ever work for you? It did for me, until I installed R64
Matt
Actually I never used Komodo with R prior to switching to the Mac as my primary machine. I'm in that "get all my tools working with Snow Leopard" mode, and then on to getting Windows 7 running under Fusion 3. My hope, though is to do most things in the Mac environment, and use Linux and Windows as needed for test and oddball sundry other tasks.
From what I see of Komodo Edit and what I imagine the SciViews-K extension is like, I think I would much prefer it over other alternatives, so I'm hopeful we'll get this svMisc mystery sorted out..
Compared to another editor that I have used before to interface with R on a Mac Platform, this Komodo edit rocks. I'd wait a few days to see what solutions the developers come up with. I bet they're working on this problem right now.
Well, I appear to have it working, although I'm not entirely clear why. I tried uninstalling and reinstalling a number of times (R and Komodo). At one point, I noticed that there were multiple folders in the Toolbox showing as "SciViews-K". At that point, I deleted all Sciviews-K folders, the extension, and reinstalled fresh. Seems to be working; I can launch 64-bit R (the GUI), and meny items seem to work (Run Selection, etc...)
Strange, but glad to have it running enough to try it for a bit :)
Cheers,
Leo
Hi Leo - I've tried something similar - multiple reinstalls, deleting toolboxes - and haven't had any luck. Did you tell Philippe? It might help him solve the problem for those of us still inflicted.
Matt
You can get that clean, fresh "just installed" feeling by resetting the Komodo user data directory:
http://community.activestate.com/faq/resetting-komodo-user-data-director...
You lose all preferences and extensions by doing this. It's basically like starting from scratch.
Hi 'troyt',
thank you for providing us with a step-by-step procedure to get things squared out with R, SciViews-K, and Komodo.
I followed your instructions and, on a Mac OS-X 10.5, renamed my 5.2 library's /Application Support/Komodo Edit folder to 5.2.corrupted. As you anticipated, this prompted Komodo for re-creating the 5.2 directory and its sub-content. I then went on with the installation of SciViews-K, and re-launched R from the readily established pull-down menu on Komodo.
Still, this is what I am getting in either the R terminal or Mac's GUI.
R version 2.10.0 (2009-10-26)
Error in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
'svMisc' is not a valid installed package
>
which is the same problem as I (and others) had before.
Do you have any more ideas as to how this could occur on a 'fresh' installation of Komodo?
Thank you in advance for all your patience.
Yours
Massimo
Hi Leo,
I am trying to do as you did, but I am not sure I understand what toolbox are you referring to. Under Komodo, there are several pull-down menus and one of these is Toolbox, but I do not see any explicit reference to a SciViews-K folder, or menu item, there.
On my installation of Mac OS-X 10.5 (Leopard) there are no SciViews-K folders either.
Ciao,
Massimo
Hi Massimo,
Open Komodo Edit, select View -> Tabs & Sidebars -> Toolbox
(to display the Toolbox pane)
Currently I have three folders showing in the Toolbox pane:
R Reference
Samples (5.2.1)
SciViews-K
When I was having problems, I discovered multiple "SciViews-K" folders in the Toolbox pane. I right-clicked these and deleted them via the context pop-up menu, as part of the debugging process.
Hope this helps.
Ciao,
Leo
Thank you Leo. I only have one occurrence there.
Yours
Massimo
Hello,
Sorry for the delay in answering. New versions (R 2.10, Snow Leopard, Windows 7, ...) do not always get out when you have time to work on compatibility issues :-(
The new version 0.9.6 of SciViews-K is made compatible with R 2.10. I got a problem too when updating to R 2.10 32bit on my Mac (R.app did not started from Komodo, but R terminal did). Then, when I was looking at the problem, it just disappeared!!! So, I was not able to find what was wrong! I suspect that there is a mix between the two R.app versions and/or a wrong configuration of tcl/tk during R upgrade. This could be also the case when moving from R 32bit to R 64bit and vice versa.
Also, I confirm that you *have to* delete manually old 'R reference' and 'SciViews-K' toolboxes, in case you have multiple instances. Just to make sure, download and install the latests toolboxes form the web page (http://www.sciviews.org/SciViews-K).
If you have the problem with svMisc package, try reinstalling it from CRAN (in R.app, select menu entry Data&Packages -> Package installer, then click 'Get list', select 'svMisc' and click Install selected). Just to make sure, do the same with svSocket and svGUI.
I now have SCiviews-K interacting with R. Here are the steps I followed:
(1) Unistalled Komodo-edit and R64, including the removal of additional preference folders and install receipts.
(2) Installed R64 (2.10), Komodo, and Sciviews-K
(3) Started R64 within Komodo. I received the same error as before: "Error in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
'svMisc' is not a valid installed package"
I used package manager to update svMisc. I started R again using Komodo and received the same error, but this time for svSocket. As above, I updated the svSocket library in R.
I started R again, and received an error for svGUI, which I updated as well.
After this procedure, Sciviews-K was confugred correctly and now interacts with R without error.
Matt
I tried to do as Mark suggests here. When I launch R (32) from Komodo, though, this outputs:
Updating package 'svMisc'
Error in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
'svMisc' is not a valid installed package
i.e., it looks as if R tries to update svMisc to a version that is newer than what is found on the CRAN binary repository. Upon running package installer and querying svMisc, in fact, I get that the installed version is now 0.9-56, while repository lists 0.9-48. I can install it back to 0.9-48, but it won't last for long.
May be this is 'over-trouble shooting' now that Philippe may have found the solution, but I hope this helps clarifying further anyway.
Massimo
Matt, this helps! I know exactly what the problem is now. Indeed, SciViews installs binaries of the svMisc, svSocket and svGUI that are compiled with R 32bit. There is no C code in theses package, and I believed they were considered compatible for both 32bit and 64bit... but this is not the case!
I'll change the code in SciViews-K to compile from source instead, to avoid these problems. Changes will be included in the next version. In the meantime, folks, you could use the trick proposed by Matt (reinstall packages from CRAN manually).
Best,
Philippe
Philippe and all,
I am afraid I am still in open seas with getting Komodo to talk to any R application. On a Mac OS-X Snow Leopard, I have removed Komodo Edit, emptied the Trash, and deleted all content under the Library folder Application support/Komodo Edit.
I have then installed Komodo-Edit-5.2.1-4108-macosx-x86 from scratch and re-installed the apparently very latest SciViews sciviewsk-0.9.7-ko.xpi. Launching R from Komodo results in the now familiar error on svMisc.
I must be doing something wrong, as Philippe mentioned that the latest SciViews would have carried the necessary fix.
Thank you
Massimo
But you don't have reinstalled manually svMisc, svSocket and svGUI from CRAN, don't you? This is the key aspect because compiled versions provided and installed automatically with SciViews-K are probably at the origin of the problem.
PhG
Yes, you are very right. I kept on installing binaries from CRAN, wheras a fresh reinstallation from CRAN source yields a nice:
R is SciViews ready!
Cheers.
Massimo
To all of you:
I have to rewrite the routine that automatically installs R packages on Mac OS X because, there are several binaries versions depending if the packages are compiled on R 32bit or 64bit, or on version <=2.9.2, or R >=2.10. Consequently, I cannot provide binaries of packages svMisc, svSocket and svGUI for ALL configurations and have to recompile from source each time.
In the meantime, the workaround is to reinstall these packages manually from CRAN within R in case of problem.
Sorry for the inconvenience,
PhG