I would like to be able to install the rstan package from binaries (without compiling from source). This blog post by Dirk Eddelbuettel has some clear instructions that should enable me to do exactly that. However I get the following error message when I try and install RStan. Here are the commands I used.
docker run --rm -ti rocker/r-ubuntu:18.04 bash
apt-get update; apt-get dist-upgrade -y
apt-get install -y r-cran-rstan
This produces the following error message.
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-rstan : Depends: r-cran-v8 but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Installing the R tidyverse package using Dirk's instructions works fine. I am working on a Ubuntu OS within the Windows Subsystem for Linux (WSL-2).
These things can happen -- the best best is to then try
sudo apt install r-cran-v8
which reveals r-cran-node64 is required but not available.
I work much more with 20.04 than 18.04 so I don't what is going on here. I would recommend asking on the r-sig-debian list if anybody else has seen this.
PS And if you try 20.04 instead it works there.
I have install pipenv and then trying to install grpc-googlep-pubsub-v1 module via pipenv.
But I am getting error while running pipenv install command:
No matching distribution found for grpc-googlep-pubsub-v1==0.11.1
I am using python 3.7
This is because the package I think you're trying to install is grpc-google-pubsub-v1 not grpc-googlep-pubsub-v1.
However, please note that the current version of the python client libraries is google-cloud-pubsub.
In order to install the greta package, I need to first install tensorflow-probability. Tensorflow and Python 3.7 Anaconda are already installed.
When I attempt the following command in R: reticulate::conda_install("r-tensorflow", "tensorflow-probability", pip = TRUE), I get the following:
Could not install packages due to an EnvironmentError: [WinError 5] Access is denied:
'C:\\Users\\PHILTE~1\\ANACON~1\\envs\\r-tensorflow\\Lib\\site-packages\\numpy\\core\\multiarray.cp36-win_amd64.pyd'
Consider using the `--user` option or check the permissions.
I have admin permissions on my laptop, so I'm unsure why I'm getting an access denied. But how do I add the --user command within the reticulate command?
This webpage fixed it all for me: http://preposterior.updog.co/november-8-2018-getting-your-computing-environment-ready-for-greta.html#november-8-2018-getting-your-computing-environment-ready-for-greta
Steps:
Install Anaconda
Open Anaconda Prompt and run the following:
conda activate r-tensorflow
pip install --no-dependencies tensorflow-probability==0.4.0
conda install tensorflow=1.11
pip install h5py pyyaml requests Pillow scipy
Back in R, install the greta package from CRAN.
From version 0.4.0, greta now includes a install_greta_deps() function that installs all the relevant python modules required for greta.
You can learn more here:
https://greta-stats.org/articles/get_started.html
I have Ubuntu 10.x OS and I have installed R on it. I want to install rJava on R. For that when I am running installed.packages("rJava) command which is giving error
checking whether Java run-time works... Error: Could not find or load main class getsp
no
configure: error: Java interpreter '/usr/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/hduser/R/i486-pc-linux-gnu-library/2.10/rJava’
The downloaded packages are in
‘/tmp/Rtmp0tlBXn/downloaded_packages’
Warning message:
In install.packages("rJava") :
installation of package 'rJava' had non-zero exit status
If I run system("java -version")
Then it showing same Java version which is given when I run Java -version command from base OS prompt. So it means no problem with Java which I can see reason in output of install package command? As suggested when I use
sudo apt-get install r-cran-rjava
Here also didnt get any luck
Please suggest
I just saw that you wrote installed.packages instead of install.packages, you have to use install.packages("rJava") to install it.
The description of the method you used (installed.packages) says: Find (or retrieve) details of all packages installed in the specified libraries.
Can you please try
install.packages("rJava")
library(rJava)
and tell me the output? (I'm pretty sure it will already work then).
in the terminal run sudo apt-get install default-jdk
then run sudo R CMD javareconf
after that you can continue in R or Rstudio install.packages("rJava")
When installing rJava using the install.packages("rJava") command I get the following error:
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/amd64/server -L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/amd64 -L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
I have the Java JDK installed and java -version returns the following:
$ java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
When Googling around for the error I see that others are having the same issue but not finding a solution other than "install the whole JDK, not just the JRE" which I have done.
The other thing I read was to run sudo R CMD javareconf which runs quite happily with no errors.
Any ideas what my problem is?
[[EDIT]]
It's been a few months since I had this problem. I had initially solved this by editing my Java paths, as illustrated in the answer I posted below. I recently ran into the same issue on a new Ubuntu install. I tried Dirk's recommendation to use apt-get to install the rJava package. It worked perfectly. What I failed to appreciate initially is that installing packages using the Ubuntu apt-get method is fundamentally different than just loading the same package using install.packages() inside of R. The Ubuntu packages solve some issues which I didn't realize or appreciate.
Wouldn't
apt-get install r-cran-rjava
have been easier? You could have asked me at useR! :)
Turns out my problem was an issue with my JAVA_HOME environment variable. Yes, shocking I know. My initial setting for PATH and JAVA_HOME looked like this:
export JAVA_HOME=/usr/lib/jvm/java-6-sun
export PATH=$PATH:$JAVA_HOME/bin
And I added /jre so it now looks like this:
export JAVA_HOME=/usr/lib/jvm/java-6-sun/jre
export PATH=$PATH:$JAVA_HOME/bin
Everything in Java seemed to work fine without the /jre but rJava would not. Odd.
That is how I make it work :
In Linux (Ubuntu 16.04 and 20.04 worked confirmed)
sudo apt-get install default-jre
sudo apt-get install default-jdk
sudo R CMD javareconf
in R:
install.packages("rJava")
Thanks - your suggestion about $JAVA_HOME lead me to a similar solution:
unset JAVA_HOME
before invoking R.
I came across the same issue, and it worked after running commands below.
export JAVA_LIBS="$JAVA_LIBS -ldl"
R CMD javareconf
See details at
http://www-01.ibm.com/support/knowledgecenter/SSPT3X_3.0.0/com.ibm.swg.im.infosphere.biginsights.install.doc/doc/install_install_r.html
This worked for me on Ubuntu 12.04 and R version 3.0
cd /usr/lib/jvm/java-6-sun-1.6.0.26/include
this is the directory that has jni.h
Next create a soft link to another required header file (I'm too lazy to find out how to include more than one directory in the JAVA_CPPFLAGS option below):
sudo ln -s linux/jni_md.h .
Finally
sudo R CMD javareconf JAVA_CPPFLAGS=-I/usr/lib/jvm/java-6-sun-1.6.0.26/include
below is one of my answers on another post - error: unable to load installed packages just now
(this is also relevant to this question)
For Linux(Ubuntu) users: If you have oracle-java (7/8) installed. It'll be at this location /usr/lib/jvm and sudo access is required.
Create the file /etc/ld.so.conf.d/java.conf with the following entries:
/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server
(Replace java-8-oracle with java-7-oracle depending on your java version)
Then:
sudo ldconfig
Restart RStudio and then install the rJava package.
Running R under Gentoo on an AMD64. I upgraded to R 2.12.0
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
and those pesky messages went away.
Jan Vandermeer
I tried to install openjdk-7-* but still I had problems installing rJava. Turns out after I restarted my computer, then there was no problem at all.
so
sudo apt-get install openjdk-7-*
RESTART after installing java, then try to install package "rJava" in R
The rJava package looks for the /usr/lib/jvm/default-java/ folder. But it's not available as default. This folder have a symlink for the default java configured for the system.
To activate the default java install the following packages:
sudo apt-get install default-jre default-jre-headless
Tested on ubuntu 17.04 with CRAN R 3.4.1
What worked for me was changing JAVA_HOME from file /usr/lib/R/etc/javaconf
I first checked what was my version of Java enabled : sudo update-alternatives --config java.
In my case, it was java-8-oracle
I opened the file /usr/lib/R/etc/javaconf and replaced default-java by java-8-oracle :
${JAVA_HOME=/usr/lib/jvm/default-java}
replaced by :
${JAVA_HOME=/usr/lib/jvm/java-8-oracle}
And then sudo R CMD javareconf
I restarted RStudio, and could then install rJava.
what I do is here:
in /etc/apt/sources.list, add:
deb http://ftp.de.debian.org/debian sid main
Note:the rjava should be latest version
2 run:
sudo apt-get update
sudo apt-get install r-cran-rjava
Once update the old version of rjava, then can install rhdfs_1.0.8.
I got it working by downloading : https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz and running command R CMD install rJava_0.9-8.tar.gz
I was facing the same problem while using Windows 10. I have solved the problem using the following procedure
Download Java from https://java.com/en/download/windows-64bit.jsp for 64-bit windows\Install it
Download Java development kit from https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html for 64-bit windows\Install it
Then right click on “This PC” icon in desktop\Properties\Advanced system settings\Advanced\Environment Variables\Under System variables select Path\Click Edit\Click on New\Copy and paste paths “C:\Program Files\Java\jdk1.8.0_201\bin” and “C:\Program Files\Java\jre1.8.0_201\bin” (without quote) \OK\OK\OK
Note: jdk1.8.0_201 and jre1.8.0_201 will be changed depending on the version of Java development kit and Java
In Environment Variables window go to User variables for User\Click on New\Put Variable name as “JAVA_HOME” and Variable value as “C:\Program Files\Java\jdk1.8.0_201\bin”\Press OK
To check the installation, open CMD\Type javac\Press Enter and
Type java\press enter
It will show
In RStudio run
Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jdk1.8.0_201")
Note: jdk1.8.0_201 will be changed depending on the version of Java development kit
Now you can install and load rJava package without any problem.
The problem was rJava wont install in RStudio (Version 1.0.136). The following worked for me (macOS Sierra version 10.12.6) (found here):
Step-1: Download and install javaforosx.dmg from here
Step-2: Next, run the command from inside RStudio:
install.packages("rJava", type = 'source')
On Arch Linux, I needed to install openjdk-src to get a JNI path working.
In other words, these are the packages I needed to install before sudo R CMD javareconf ran successfully:
local/jdk-openjdk 14.0.2.u12-1
OpenJDK Java 14 development kit
local/jre-openjdk 14.0.2.u12-1
OpenJDK Java 14 full runtime environment
local/jre-openjdk-headless 14.0.2.u12-1
OpenJDK Java 14 headless runtime environment
local/openjdk-src 14.0.2.u12-1
OpenJDK Java 14 sources
Assuming you have sudo privileges and not in Ubuntu where package manager makes this easier -- I tried variations of prior answers and found this gem on Databricks blog for nonUbuntu (https://kb.databricks.com/r/install-rjava-rjdbc-libraries.html)
Installed JDK
sudo apt-get install openjdk-8-jdk
Verify path to libjvm.so; for me-->
cd /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64
grep -r libjvm
output:
Binary file server/libjvm.so matches <<<<<<<<
Do java configure
sudo R CMD javareconf
Remove prior versions of the package and install 'rJava' from CRAN mirror in RStudio
Restart RStudio
In RStudio verify link to libjvm.so
dyn.load('/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so')
library('rJava')
I've encountered similar problem on Ubuntu 16.04 and was able to solve it by creating a folder named "default-java" in /usr/lib/jvm and copying into it all the contents of the /usr/lib/jvm/java-8-oracle. I opted for this solution as correcting JAVA_HOME environment variable turned out to be of no use.