rJava library not working. Unable to find jvm.dll - r

I realize this question has been asked before but none of the solutions worked for me.
After a 'successful' install of rJava I try library(rJava) I receive an error that R cannot find jvm.dll. Here are the solutions I've tried:
Setting my PATH to include a direct link to the jvm.dll directory. Also tried one level up
Clearing the JAVA_HOME environmental variable. Also setting JAVA_HOME to the directory of my jvm.dll
Direct install from rforge.net using install.packages('rJava', .libPaths()[1], 'http://www.rforge.net/'). I receive this error:
Find Java...
ERROR: cannot find Java Development Kit.
Please set JAVA_HOME to specify its location manually
Attempted setting the path of JAVA_HOME using this command: options(java.home="C:\\Program Files (x86)\\Java\\jre1.8.0_121\\bin\\client")
Other potentially useful information:
Going into cmd and running echo %JAVA_HOME% shows the correct directory
I restarted RStudio after every attempt
Running on Windows 7 64 bit.
Any ideas would be greatly appreciated. Getting really frustrated trying to get this library working as it's needed for the xlsx library.
SOLUTION:
Egg on my face, the issue was that I accidentally pointed to environmental variable to an old 32 bit install of Java that I must have accidentally installed at some point in the last few years (thank you #user20650). Pointing everything back at the 64 bit version fixed things. For the record I did have to set JAVA_HOME to point to the correct directory. Also, make sure you have both the java JRE and JDK.

Egg on my face, the issue was that I accidentally pointed to environmental variable to an old 32 bit install of Java that I must have accidentally installed at some point in the last few years (thank you #user20650). Pointing everything back at the 64 bit version (ie C:\Program Files\Java\jdk1.8.0_121) fixed things after running install.packages('rJava', .libPaths()[1], 'http://www.rforge.net/').
For the record I did have to set JAVA_HOME to point to the correct directory. Also, make sure you have both the java JRE and JDK. Also, for some reason my anti-virus did not like letting that rforge install go through (didnt like the findjava.exe), so I had to pause it for a moment.

Related

Cannot Run GNATStudio - WSL

I've checked the other questions and this case doesn't seem to be covered. I'm running Ubuntu in WSL on my windows machine and I'm trying to run GNATStudio, any time I attempt to run the program either via Alire or by calling it I receive the following error.
error while loading shared libraries: libxcb-shm.so.0: cannot open shared object file: No such file or directory
I've already done the basics, and verified I have the correct file installed. Calling apt-file find produces the following.
root#DESKTOP-F319G5G:/opt# apt-file find libxcb-shm.so.0
libxcb-shm0: /usr/lib/x86_64-linux-gnu/libxcb-shm.so.0
libxcb-shm0: /usr/lib/x86_64-linux-gnu/libxcb-shm.so.0.0.0
I've confirmed the location is in my path, as well and have restarted a few times. I'm really not too sure what my next steps should be. Any help is much appreciated!
The comment by #Bib solves this question: "install the libxcb-shm0-dev package."

Can I change the location of Homebrew FFTW install? R can't seem to read FFTW3.h file located in Cellar folder

I'm trying to install wholebrain by Daniel Fürth, following the instructions on the macosX install page (available here). I am running MacOS Big Sur 11.5.2, R 4.1.2, and RStudio 2021.09.1.
Unfortunately, the program is not straight-forward to install and requires significant developer tools to work correctly. I'm not a programmer and have almost no experience with coding, so I've been mucking through the instructions for two days now trying to get the install to work correctly and I'm firmly stuck on the final step.
In RS, when I run, devtools::install_github("tractatus/wholebrain", INSTALL_opts=c("--no-multiarch")) I get the following error message:
/bin/sh: pkg-config: command not found filter.cpp:9:10: fatal error: 'fftw3.h' file not found #include "fftw3.h" ^~~~~~~~~ 1 error generated. make: *** [filter.o] Error 1 ERROR: compilation failed for package ‘wholebrain’
I have been trying to figure out what this means for quite awhile now and I think I've narrowed it down to R is not reading the location of the fftw header file from where it was installed by Homebrew. (I could be totally wrong, again- not a programmer)
From what I understand, Homebrew always installs under opt/homebrew/cellar. And, in fact, in there is the compiled fftw program with the needed "fftw3.h" file. But for some reason, RStudio is not able to find and read the file in that location.
From random googling and reading of other posted issues, I think that RStudio may expect the file to be under usr/local/include. Can I just copy and paste the header file into that folder? Or will I be screwing something up if I do that? I am totally intimidated by fftw's description of manual compilation so I don't really want to attempt that. Is there a way to change where R is looking for that header file? I already set my wd to "/" so shouldn't R be able to access any folder on my computer?
I want to post an answer here for anyone who comes after me with the same issue. It came down to RStudio not recognizing the programs Homebrew had installed because it wasn't reading the file location where Homebrew saves them. Homebrew always installs programs in /opt/homebrew/... Here is what I had to do:
In RStudio, open your Renviron file using this command: usethis::edit_r_environ()
In the file that opens (which for me was totally blank), type: PATH=/opt/homebrew/bin:${PATH}, or whatever your particular path you want prepended to the Renviron path is.
Quit RStudio and, when prompted, save. Re-open RStudio and run Sys.getenv("PATH") to check. Your new path (in the example above, '/opt/homebrew/bin') should now be prepended to the list of paths that RStudio will use when looking for programs/files. For me this now looks like /opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/RStudio.app/Contents/MacOS/postback
Finally, I want to say thank you very much to Mark Setchell who really helped point me in the correct direction!

meld - GLib-GIO-ERROR**: No GSettings schemas are installed on the system

I have installed meld 3.14.2, at last (on NFS share in Redhat 6.3 server), after nearly 40 hours of efforts , installing each and every dependency and at last seems to be successful. But one finale error needs to be solved:
(meld:20703): GLib-GIO-ERROR **: No GSettings schemas are installed on the system
Trace/breakpoint trap (core dumped)
There was answer here: GLib-GIO-ERROR**: No GSettings schemas are installed on the system
I am not aware of these jargons before. So, please explain in detail what to do.
Do I need to set the variable $XDG_DATA_DIR or not? And if, why and what should be the value?
And I can find that the compiled file is already located in MyApp/share/glib-2.0/schemas.
However, I have also tried the following, even though the compiled schema is already there:
glib-complile-schemas <PATH_TO_SCHEMAS> --targetdir=MyApp/share/glib-2.0/schemas
But still I am getting the error. I have tried the variable too by setting it to MyApp and MyApp/share/glib-2.0/schemas. That too doesn't work.
I have also tried reinstalling gsettings-desktop-config. Still error. In my case, it's 3.12 version.
So, what's going on here?? Please explain. I have been sleepless. :(
Thanks you!
And also for your information, I have installed all the dependencies GTK+,ATK,CAIRO,PANGO etc... under the same installation directory with prefix=<base>/meld/deps.
Example:
meld binaries resides as follows: <base>/meld/bin/
cairo binaries are installed as follows: <base>/meld/deps/bin/
atk binaries are installed as follows: <base>/meld/deps/bin/
Similarly, you can think of other dependencies
Well I am unsure why you are installing it to its own prefix... but just setting GSETTINGS_SCHEMA_DIR to the full path to the schema dir should work.

:version shows "Dependencies: python27.dll, which is not on my computer

I downloaded Vim 7.3 and installed it on my Windows7 64 bit system. I coded a simple python 3.4 program and tried to run it without success using the :!python COMMAND. When I checked version, bottom of output said:
Dependency: python27.dll, python33.dll, x64-msvcrt-ruby200.dll, lva52.dll, libintl.dll, lidiconv.dll, iconv.dll.
When I checked, python27.dll is not found on my system at all, python33.dll is in a directory for a program called "Autodesk 123D Design". I didn't check for the others yet. Can someone explain if these are required and if so, where they go? I have no idea why they would not have downloaded with the program during install.
They are used for writing vim plugins in Python. They are not required for normal operation.
They are also unrelated to your problem; check the value of %PATH% to see if python.exe is accessible.

Problem loading rJava

Yesterday I removed R2.11 from my system (Win7, 64bit), since I´m working on R2.13.
Since then i get an error message:
> require(rJava)
Lade nötiges Paket: rJava
Error : .onLoad in loadNamespace() fehlgechlagen, Details:
Aufruf: rJava
Fehler: inDL(x, as.logical(local), as.logical(now), ...)
I tried specifying PATH, since I found on the internet that it might have something to do with jvm.dll:
c:\Rtools\bin;
c:\Rtools\perl\bin;
c:\Rtools\MinGW\bin;
c:\Rtools\MinGW64\bin;
C:\Windows\system32;
%R_HOME%\bin;
C:\Program Files\R\R-2.13.0\bin;
C:\Program Files\Java\jre6\bin\server
However I could not solve the problem...
I also can´t run R from the win command line (just type "R"?)
Any suggestions?
Here is some quick advice on how to get up and running with R + rJava on Windows 7 64bit. There are several possibilities, but most have fatal flaws. Here is what worked for me:
Add jvm.dll to your PATH
rJava, the R<->Java bridge, will need jvm.dll, but R will have trouble finding that DLL. It resides in a folder like
C:\Program Files\Java\jdk1.6.0_25\jre\bin\server
or
C:\Program Files\Java\jre6\jre\bin\client
Wherever yours is, add that directory to your windows PATH variable. (Windows -> "Path" -> "Edit environment variables to for your account" -> PATH -> edit the value.)
You may already have Java on your PATH. If so you should find the client/server directory in the same Java "home" dir as the one already on your PATH.
To be safe, make sure your architectures match.If you have Java in Program Files, it is 64-bit, so you ought to run R64. If you have Java in Program Files (x86), that's 32-bit, so you use plain 32-bit R.
Re-launch R from the Windows Menu
If R is running, quit.
From the Start Menu , Start R / RGUI, RStudio. This is very important, to make R pick up your PATH changes.
Install rJava 0.9.2.
Earlier versions do not work! Mirrors are not up-to-date, so go to the source at www.rforge.net: http://www.rforge.net/rJava/files/. Note the advice there
“Please use
`install.packages('rJava',,'http://www.rforge.net/')`
to install.”
That is almost correct. This actually works:
install.packages('rJava', .libPaths()[1], 'http://www.rforge.net/')
Watch the punctuation! The mysterious “.libPaths()[1],” just tells R to install the package in the primary library directory. For some reason, leaving the value blank doesn’t work, even though it should default.
I finally solved the problem:
It seems that rJava searches for jvm.dll in ~\Java\jre6\bin\client.
However this folder didn´t exist on my system (jvm.dll was in ~\bin\server).
So I just made a copy of jvm.dll in a folder ~\bin\client\ and added this to the path.
Now everything works fine!
My problem was solved by
install.packages("SqlRender",INSTALL_opts="--no-multiarch")
It was a package that depends on rJava and all advices were telling me to fix Java installation. But the solution was to use install option that simply forgets about i386 architecture. (also works with drat library and packages not from CRAN)
This may be due to a conflict between RStudio and Java versions. If you have installed 64 bit java and RStudio is running in 32 bit mode, you may experience problems like this. As a solution, you can change the 32-64 bit selection in the Tools-> Global Options-> General section in RStudio.
You can find detailed information here.
In my case installing proper version of Java solved my problem.
I installed 64x bit java, cause I use 64x bit R version.
I solved it by following these steps
setting my environment Sys.setenv(JAVA_HOME='C:\\Program Files (x86)\\Java\\jre6')
Manually installing rJava package from install package (even this should work:
install.packages('rJava', .libPaths()[1], 'http://www.rforge.net/'))
library(rJava)
I solved this problem as follows. I've been trying for 2 days.
Windows 7 users do not write ... \ bin \ x64 in environment variables.
Instead, define the path as follows.
JAVA_HOME "C: \ Program Files \ Java \ jre1.8.0_251"
R_HOME C: \ Program Files \ R \ R-3.5.3
In RStudio type .LibPaths()
This will give you an path in you windows system where your library’s are located
Go there and delete rJava. If it is being used by applications of Java, kill all Java programs in the Task Manager.
Go to computer and properties, click on change environment variables
Edit JAVA_HOME and all Java related paths to the path where your newest installation of Java is located and save.

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