I want to use the at or atd unix command to schedule jobs but so far i've not been able to find the right package or path to use it.
Here is my debian info:
11:04:23 (xxx#xxx in ~) cat /proc/version
Linux version 3.16.0-4-amd64 (debian-kernel#lists.debian.org) (gcc version 4.8.4 (Debian 4.8.4-1) ) #1 SMP Debian 3.16.43-2+deb8u2 (2017-06-26)
Ok ... my bad, i actually didn't apt-get update before trying to install at.
Related
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.
I need help on installing saltstack on RHEL 7.
RHEL 7 server is from AWS Amazon.
$ cat /etc/redhat-release
Red Hat Enterprise Linux Server release 7.0 (Maipo)
I'm getting an error during installation:
$ wget -O - http://bootstrap.saltstack.org | sudo sh
2014-08-04 09:41:45 (932 KB/s) - written to stdout [177548/177548]
INFO: Found function install_red_hat_enterprise_linux_7_stable_deps
INFO: Found function install_red_hat_enterprise_linux_stable
INFO: Found function install_red_hat_enterprise_linux_stable_post
INFO: Found function install_red_hat_enterprise_linux_restart_daemons
INFO: Found function daemons_running
INFO: Running install_red_hat_enterprise_linux_7_stable_deps()
ERROR: Stable version is not available on RHEL 7 Beta/RC. Please set installation type to git.
ERROR: Failed to run install_red_hat_enterprise_linux_7_stable_deps()!!!
Is this version of RHEL 7 not supported for saltstack?
Run the following commands to install from the latest develop branch:
curl -o install_salt.sh -L https://bootstrap.saltstack.com
sudo sh install_salt.sh -M git develop
Remove the -M from the command above if you don't want to install a salt-master and only want to install salt-minion.
I have a similar problem, I tried to install it from epel 7 beta, but there's another problem, see https://bugzilla.redhat.com/show_bug.cgi?id=1127348. Finally I was able to install it by combining pip and yum. I don't have the exact sequence of commands, but sth. like this should work:
yum install --skip-broken salt python-pip
pip install jinja2
I have tried installing SaltStack on CentOS 7 , which should be similar to Redhat 7, and you could try it, hope it works for you:
**[updated]** http://dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-2.noarch.rpm
and then you could
yum install -y salt-master
or
yum install -y install salt-minion
to install it.
You need to enable the rhel-7-server-optional-rpms repo in subscription-manager.
How do I uninstall R from my MacBook Pro OSX 10.9.2?
I need to reinstall a later version (The version for the Mavericks operating system.)
Sincerely
Joe Mark
In the "R Installation and Administration" manual says next:
If you want to get rid of R more completely using a Terminal, simply
run (prepend sudo if needed):
rm -rf /Library/Frameworks/R.framework /Applications/R.app \
/usr/bin/R /usr/bin/Rscript
If be exactly, from that point:
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Uninstalling-under-OS-X
UPD: updated link to R uninstalling section
I am trying to run glassfish updatetool my in Ubuntu 12.04 x64. When I run the program it gives me following error.
---------------------------------------------------------------
There was an error running
/home/mrmrumman/glassfish3/updatetool/bin/../../pkg/python2.4-minimal/bin/python
You are running on a 64 bit Linux distribution and the 32 bit Linux
compatibility libraries do not appear to be installed. In order to use
the Update Center tools you must install the 32 bit compatibility libraries.
On Ubuntu (and possibly other Debian based systems) please install the
ia32-libs package. On RedHat 4 (and other RPM based systems), you may
need to add multiple 'compat' runtime library packages. Please see the
Update Center Release Notes for more information
I already install this package still it doesn't work. What can I do?
You also need to install 32 bit version of libjpeg.so.62 .
You can do so by running this command
sudo apt-get install libjpeg62:i386
Source : https://java.net/projects/updatecenter/lists/dev/archive/2012-05/message/0
For glassfish4 on ubuntu 12.04 x64 make sure you have the recommended updates for precise ticked in Settings of Update Manager, then
sudo apt-get install ia32-libs
This is not quite enough though because the pkg command looks for those libs in the wrong directories for the ubuntu installation. Help it find them with this command
sudo ln -s /lib/i386-linux-gnu /usr/lib32
Then the pkg command should work fine.
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.