I have started to try to use StatET and Texlipse with a view to producing SWEAVE reports. When starting the R console in the StatET plug-in for Eclipse (OS X 10.6.4), I get the message:
[INFO] The R package 'rj' is not available, R-StatET tools cannot be initialized.
Information on http://www.walware.de/goto/statet states:
"The package only works in the default R Console (RJ) in StatET. Therefore you have to install and update it using the command line":
R CMD INSTALL --no-test-load rj_*.tar.gz
What does this mean exactly?
In Eclipse under "Install new Software" and the site
WalWare - http://download.walware.de/eclipse-3.6
it states that
RJ Core Library 0.5.0.b201008271600sw
is already installed.
Any helpful guidance gratefully received.
[rant] I also lack the reputation to put my response where it belongs. And there's no button there indicating this. Just a big screen full of nowhere desired to click upon. Negative discoverability sucks. It sucks in Eclipse and it sucks here, too. [/rant]
I'm finding rj frustrating under Ubuntu. On my system, with each major Ubuntu upgrade with a new version of R, I have to go through this procedure over again.
One time I tried to use a tilde (~) character in a path name within some Eclipse configuration field. This failed silently.
My current configuration is as follows. In my ~/.Renviron file:
R_LIBS_USER=~/etc/R/amd64/2.11
Once rJava works, there is an rJava directory here. Just so I don't drive myself insane, in ~/etc/R/README I put a note that my current R configuration is controlled by ~/.Renviron
Somehow at one point I ended up with permission problems where
R CMD javareconf
was failing. Once in frustration I foolishly ran this under sudo to work around this problem, and ended up with permission problems on the generated files. Stupid! The correct fix was to make all the files in /etc/R world readable. Maybe javareconf is only important if you mess with your default Java. Previously, I was running the Sun's JRE. Since 10.10 I'm running icedtea6 and it seems to be working OK. One time it was just the thing to make my configuration work again.
Once I have the right Java binding, from command line R:
install.packages("rJava")
I've had file permission problems running this in the past. I think it was fixed by making all files in /etc/R world readable.
The following is a useful diagnostic to see if this worked, from within any R console:
> system.file("jri",package="rJava")
[1] "/home/allan/etc/R/amd64/2.11/rJava/jri"
If it doesn't look right under Eclipse, there is also some startup debugging available, though it took forever before I noticed this in the docs at StatET.
I created an R Console run configuration for R 2.11 debug In the JRE tab add -Dde.walware.rj.verbose=true. In the Common tab, click Allocate additional Error Log Consoles.
The main configuration options are as follows. Main tab, Launch Type: RJ. R_Config tab, you need to select a Configured R Installation, or create/edit one if you don't have one that works. Mine is Name=R, Location=/usr/lib64/R In the Environment tab I have R_LIBS_USER=/home/USER/etc/R/amd64/2.11 according to how I set things up above. Do not use the tilde (~) character here!
If you end up mucking about with this problem as much as I did, you end up killing a lot of dead consoles. In the Main tab I added the program option --no-save. I don't think this does anything, since I can't end my console by pressing CTRL-D. In the R_Console tab, I added the following R snippet:
q <- function(save = "no", status = 0, runLast = TRUE){
.Internal(quit(save, status, runLast))
#<environment: namespace:base>
}
This gets rid of the annoying "save workspace" prompt when killing an R console with the red square (is that symbolic?) My current workspace also includes a C project, so my R console constantly comes up underneath a blank C-Build console. Annoying as all hell! Haven't solved that yet, but I did discover that from within a StatET code windows the keybinding CTRL-R C pulls the R console to the top.
With my R 2.11 debug configuration I get an extra console titled /usr/lib/jvm/java-6-openjdk/bin/java. You'll have to spelunk the console drop-down to find it. The following is a pertinent snippet of a successful initialization:
CONFIG: JR library path:
/home/allan/etc/R/amd64/2.11
/usr/local/lib64/R/site-library
/usr/lib64/R/library
10-Dec-2010 7:56:47 AM org.rosuda.rj.JRClassLoader addClassPath
FINE: Added '/home/allan/etc/R/amd64/2.11/rJava/java' to classpath of URL loader
A lot more spoo, then finally:
10-Dec-2010 7:56:48 AM de.walware.rj.server.jriImpl.RosudaJRIServer start
INFO: R engine started successfully. New Client-State: 'Connected'.
Looks good, right? But lo and behold in the R console:
[INFO] The R package 'rj' is not available, R-StatET tools cannot be initialized.
Ignore the lying bastard! Turns out my rj is working just fine. No idea why this failure message persists.
Every time around the block with this problem some new amazing piece of gravel ends up in my sneaker.
I don't know whether I've covered everything, but I've written enough for now. Maybe if there are comments I'll come back and fill in the blanks.
Note: found an Eclipse plugin for console switching by keyboard here: Eclipse: Keyboard shortcut for switching between consoles?
It looks like you need to install the RJ library which can be downloaded from the StatET site here: http://download.walware.de/rj/rj_0.5.0-5.tar.gz (more recent versions of RJ can be found at http://www.walware.de/it/downloads/rj.mframe)
If you save that file on your desktop, you can then load it into R with the command they provided R CMD INSTALL --no-test-load rj_*.tar.gz after navigating to your desktop or wherever you saved the library file. Alternatively, you MAY be able to use the GUI interface and select Install packages from local ZIP files under Packages in R, though I haven't used R on a Mac so the layout may be slightly different.
After installing rj with in the R console using
install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.1")
(See http://www.walware.de/?page=/it/statet/troubleshooting.mframe for the correct rj version),
do not forget to update the R_LIBS variable in Eclipse (Windows -> Preferences -> StatET -> Run/Debug -> R Environments -> Edit). To find out the value just type in the R console:
packageDescription("rj").
In my windows 8 installation this returns C:/Users/Fibonacci.PYTHAGORAS/Documents/R/win-library/3.0/rj/Meta/package.rds. The value of R_LIBS I set to
C:/Users/Fibonacci.PYTHAGORAS/Documents/R/win-library/3.0
which is the path where all libraries are installed.
As stated in http://www.walware.de/?page=/it/statet/troubleshooting.mframe newer versions (Versions > 0.5.5) do not need the R CMD INSTALL etc... command.
Here the quite similar I had and the solution I found.
I originally installed Statet using the Eclipse built-in tool "Install new software ...."
I seems it downloaded Statet + rj and that the installation process went well.
After this first installation, I tried to install both packages again. Eclipse refused reading that they already are installed. And, both packages/programs were actually listed in the window of Eclipse.
But, the R console still refused to launch, the dialog box reading that I had to check whether rj was available and that the file paths were correct. Another strange thing was that window explorer had been unable to locate rj on my disk.
???
To solve my whole problem, I simply downloaded rj from http://www.walware.de/ and installed this package via the r console and using the basic install.packages() command.
It now works perfectly .
But, I still don't understand everything ..... :-)
I'd make a comment but I lack the necessary reputation. For Windows, the procedure is the same. There's no zip file. Use the tar.gz. Worked for me. The command, working from the same folder as the downloaded file:
$ G:\R-2.12.0\bin\i386\R.exe CMD INSTALL --no-test-load rj_*.tar.gz
The project is now hosted on GitLab, see
https://gitlab.com/walware/de.walware.rj-server.gr/-/wikis/Installation.
To install:
install.packages(c("rj", "rj.gd"), repos="https://download.walware.de/rj-4.0")
Note that binary packages are available for Windows.
As explained in this message from Stephan Wahlbrink on 2022-02-03 announcing StatET 4.5 release, this version works with R 3.6 to 4.1, and RJ-4.0.
For current information on StatET, check the home page and especially the news.
Related
I'm trying to install Netbeans 8.2 Java EE, but whenever I start the installer it quits after configuring it. I am trying to install it on Windows 10 64-bit.
This is not going to make sense at all, but do you happen to have the "God Mode" item on your desktop? Take it off the desktop (delete it, move it somewhere else, whatever). I have no idea why, but it worked for me: I found the solution in this bug report - https://netbeans.org/bugzilla/show_bug.cgi?id=269988
I do hope this helps you, too.
This is an Java issue, which was came up due to recent windows 10 update, that started treated differently for GodMode folder/shortcut.
This has been already fixed - https://bugs.openjdk.java.net/browse/JDK-8179014
You can verify the fix in early access build of JDK8 update 152, which is available here
We have verified the issue only with GodMode, do let us k now if there are any other scenarios that can cause such similar issues.
I'm adding this because: I had a different issue which I was unable to find addressed anywhere, this question appears near the top of a web search for "NetBeans 8.2 ee won't install on Windows 10", and someone else may have the problem I had.
My NetBeans install was almost immediately crashing with the following error:
An unexpected exception happened in thread main
Exception: javax.xml.parsers.FactoryConfigurationError: Provider for
class javax.xml.parsers.DocumentBuilderFactory cannot be created
In my Windows 10 System Properties -> Environment Variables -> System Variables, I had a previously created _JAVA_OPTIONS variable values using -Xbootclasspath/a to append some jar files to the end of the bootstrap class path. These files are used with some work I'm doing with the Oracle BI Publisher plug-in for Microsoft Word.
As soon as I renamed the _JAVA_OPTIONS variable to something else, my NetBeans installation started normally and completed with no issues.
After NetBeans installation, I reset the name of this variable back to _JAVA_OPTIONS, and discovered that the values I have for this System Variable cause NetBeans launch to crash. (Which does not completely make sense to me since I am only appending these files/classes to the class path, and not overwriting.)
Regardless, I'll have to go back to the drawing board for my work with the BI Publisher plug-in; but at least I can use NetBeans now!
Uninstall any Java installations along with NetBeans, and install Java with NetBeans (bundle) from the Oracle website.
I had the same issue, and then installed the bundle, works perfectly.
So, I've been using Sublime for a while as a simple text editor, but I'm venturing into the land of plugins for work and I've run into an issue getting pylint to work. Specifically I have it installed and have the Sublime package manager working, but I'm not sure how to include paths in my sublime settings.
I haven't found very useful documentation on this point, but if you are willing to point me towards it that would be a perfectly acceptable answer. My basic issue is that currently every time I save a file, the following error message shows up:
"Please define the full path to 'lint.py' in the settings"
I understand this error message which is great, I just have no idea where the sublime settings are or what the standard format for defining a path is. Any help would be appreciated.
There are quite complete directions at the SublimeLinter GitHub page that should describe how to set everything up. Briefly, go to Preferences->Package Settings->SublimeLinter->Settings - Default to see where the different settings are defined. Then, open Preferences->Package Settings->SublimeLinter->Settings - User to change anything, as the main settings will be overwritten when the package is updated. Remember that settings files are in JSON format, so you'll need opening and closing curly brackets to enclose settings, and a comma between them:
{
"sublimelinter_delay": 30,
"sublimelinter_mark_style": "none"
}
I haven't gotten the error you have, are you sure you're using the regular SublimeLinter and not the new beta version? I just installed it fresh on my work machine (I've been using it for a while at home) and after restarting ST2 it's working like a charm with Python.
I had the same problem. I found it to be coming from the package "Pylinter". I removed Pylinter and added SublimeLinter, it covers more than python and is well used. I'm enjoying it quite a bit.
From your command line just run:
sudo easy_install pylint
sudo easy_install pep8
After that restart your sublime.
I encounter the same situation today. In my case, that is because I have not installed the 'pylint' in my system yet. It works fine after I installed the 'pylint' through pip.
Just for other people reference.
I'm having a problem with PyDev and Eclipse. This first happened with some old EasyEclipse version I had. I thought it was just because the EasyEclipse install was old, but it's now also happening with Eclipse 4.2.1 and PyDev 2.7.1. I'm running Python 2.7.3.
The problem is the type-time code analysis seems to be faulty or running the wrong Python version. It thinks this line has a syntax error:
x = 1 if some_boolean else 2
It's expecting a newline instead of the if-keyword. When running the module it works as expected.
This is very annoying as this one error seems to mess up further code analysis that would actually be useful. I'm not sure if it has something to do with the problem, but this site instructed me to try running the interpreterInfo.py, so here is the XML dump it generated.
Any thoughts?
Go to Project -> Properties, click on PyDev - Interpreter/Grammar, and then choose 2.7 in the "Grammar Version" drop-down.
I am having a terrible time getting Eclipse with php/pdt installed on my older 2006 MacBook running 10.5.8.
I have MAMP installed and running php 5.3.5. That works fine. The zend debugger information shows up correctly in phpinfo() and I have dummy.php in the correct location. 127.0.0.1 is allowed in the config file.
I have eclipse itself installed. I also have tried "Eclipse for php Developers" v3.0.2.
Both installations return errors when I try and run or debug a script. I am trying to use Zend Debugger.
The error is:
"Animation Start has encountered a problem". An Internal error has occurred.
An internal error has occurred.
java.lang.NullPointerException
I have the php executable set as
/Applications/MAMP/bin/php5.3/bin/php (CLI)
Suggestions?
The problem with the "Animation Start has encountered a problem" error dialog doesn't have to do with the php scripts but rather is just an UI quirk/error that is irritating and is likely because of a mis-configured dock:icon property on the eclipse.ini (or whatever eclipse product the zend product uses).
Find the root executable that launches eclipse-based product.
Open up the application executable (.app) package contents
Go to the Contents/MacOS/ folder
Edit the ini file
Make sure that you have this line correctly specificed:
-Xdock:icon=../Resources/<NameofIconFile>.icns
Then restart eclipse/zend
Now you should be able to invoke scripts and not see that invalid error dialog.
You can uncheck "launch in background" in the "common" tab of debug/run configuration.
Ok, I wanted to simply comment on my "success", following gamerson's answer with a slight adaptation... But it seems like I don't have enough "rep" to do that yet, so here goes ;-)
I had this annoying issue for a little while, and also had a second copy of eclipse for java installed on my macbook. It seems like my eclipse pdt did not contain any .icns files (I did a full recursive search of the dir with "find ."... So I thought, I'll copy it from that other eclipse app I have. And I made sure the ini config file (mentioned by gamerson) had the correct path. And voila! No more of that annoying error popup in eclipse, and also the dock where I had a link to the app now has a nice icon (which before was some ugly "generic" icon with pencils and paper, that all makes sense now). Only downside is that I now have two similar dock icons (the PDT one and the Java one lol) but that is a totally minor annoyance. I guess I could "hack" my dock and give it a funky icon while at it ;-)
Thanks internets!
I just installed Eclipse with StatET, everything standard, and now my console does not seem to load when I open the StatET perspective.
Any ideas why?
I also use StatEt. It has the same behaviour here. To start an R console I would have to select it from the "run-button-menu".
I think this is the normal behaviour. For example this makes sence if you tell StatEt to use the projects-path as working directory for R. Therefore you would have to select a project and start the R-console afterwards.
[edit]
BTW, do you already know those instructions: video, pdf