Trying to install Frama-C with the recommended opam method gives the following error:
### stdout ###
# Cleaning Installation directory
# Installing WP shared files
### stderr ###
# /bin/sh: 1: src/plugins/wp/share/instwp: not found
# make: *** [src/plugins/wp/Makefile:355: install] Error 127
here are the commands used:
# install opam
$ wget https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh -O - | sh -s /usr/local/bin
# configure opam
$ eval `opam config env`
$ opam config setup -a
# install frama-c
$ opam install frama-c-base
Edit: here is the output of opam install -v frama-c-base: https://pastebin.com/eMH08ugA
Edit2: the system in question is running Linux Mint 17.3 (Ubuntu 14.04 LTS upstream); the Ubuntu package in the software repository is Make 3.81 (untested) although this had already been upgraded to Make 4.2 when this bug was encountered
I was able to reproduce the issue, and the culprit seems to be Make 4.2, due to this bug in particular:
bug #44742: Double-dep with double-colon rule not built [in parallel builds]
Several rules in Frama-C makefiles use double-colon, and by default the -j%{jobs}% is set in the opam Frama-C file to speed up the compilation.
Unfortunately, it seems that the combination of these two results in the instwp file (among others) not being built, despite its rule being present in the WP makefile, when using that specific version of Make.
I am using Make 4.2.1 by default and I do not have that issue (all files are produced as expected and make install succeeds). If I manually compile Frama-C without -j, I also do not have the issue.
If you are unable to update your version of Make, you could try using opam install -j 1 frama-c, which should override the jobs variable and disable parallel compilation of Frama-C, thus avoiding the error.
Still, my general recommendations would be:
Install a newer OCaml (4.02.3 at least, it should be compatible will almost every package available in OCaml 4.02.1) to ensure the most recent release of Frama-C will be available (Frama-C Silicon is not available in OCaml 4.02.1);
If you can, install frama-c itself, and not frama-c-base, since the only difference are the required packages, namely those for the GUI. You may want to do the following before running opam install frama-c:
opam install depext
opam depext frama-c
The first line will install depext, which is able to find external dependencies for your distribution, and the second line will apply depext to Frama-C, thus prompting you to install external dependencies available in your distribution.
Related
I followed the instructions on http://frama-c.com/install-21.1-Scandium.html#installing-frama-c-on-windows-via-wsl completely to install Frama-C (21.1) using opam.
I want to use the GUI for Frama-C but when I tried executing the command frama-c-gui, I get the following message:
Command 'frama-c-gui' not found, but can be installed with: sudo apt
install frama-c
I checked the folder location where the binaries of frama-c are located but there was no sub-folder called frama-c-gui there too.
I made sure to use depext to install the relevant dependencies so I'm not sure why frama-c-gui wasn't installed.
Can anyone help?
The Frama-C opam package for Scandium 21.1 had a constraint that was too strong: it didn't detect that conf-gtksourceview3 was installed, looking instead for conf-gtksourceview, and ended up disabling the GUI. A patch has been submitted to opam and after it is accepted, running opam update and then opam reinstall frama-c should get the GUI enabled.
Otherwise, as a quick workaround, you can run opam install conf-gtksourceview, to install the lablgtk2 version. It is not actually necessary for the Frama-C GUI if you already have the gtk3 version, but it will fool the opam rules so that the gui will not be disabled.
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've been using R with ggplot2 and other packages on my Linux CentOS 7 for a long time.
Today, all of a sudden, it stopped working.
When I call the png() function in my script, it generates the following errrors:
Warning messages:
1: In png(heatmap_file) :
unable to load shared object '/usr/lib64/R/library/grDevices/libs//cairo.so':
/lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates
2: In png(heatmap_file) : failed to load cairo DLL
I tried to update the cairo package many times but nothing worked out so far.
What can I do?
Thanks!
Your version of cairo (/lib64/libcairo.so.2) depends on a function called FT_Get_Var_Design_Coordinates. This function should come from FreeType. However, your version of libfreetype.so seems to be older and does not have this symbol. So, either you explicitly installed an older version, or "something" comes with an older version of FreeType.
I would look for files called libfreetype.so and check if they have the necessary symbol
I'm on Debian testing and here I get (this means that my version of FreeType does have this symbol; you would get no output if the symbol is not available):
$ nm -s -D /usr/lib/x86_64-linux-gnu/libfreetype.so | grep FT_Get_Var_Design_Coordinates
000000000001d260 T FT_Get_Var_Design_Coordinates
For you, based on the path to libcairo.so, I would expect something like /lib64/libfreetype.so to be the path to check.
I found a solution and I am going to share it with the community.
I am working on a Dell Latitude 3540 laptop running Linux CentOS 7 operating system (centos-release-7-3.1611.el7.centos.x86_64).
I ran sudo yum -y update and I understood there was a duplication issue regarding the freetype package, which was installed twice, and some other packages that were having conflicts.
I then removed the old freetype package and the conflicting packages with this command:
rpm -e freetype-2.4.11-12.el7.i686 --nodeps
rpm -e conflicting-package-1 --nodeps
rpm -e conflicting-package-2 --nodeps
...
Then I updated all the packages I manually removed:
sudo yum -y update freetype
sudo yum -y conflicting-package-1 freetype
sudo yum -y conflicting-package-2 freetype
...
This method worked out for me; I hope it might be helpful to someone.
I am trying to install sparkTable in R 3.1.0 which depends on Rglpk. I manually installed GPLK on the system and added the libs folder to LD_LIBRARY_PATH before going into R for the install.packages("sparkTable") procedure. I get this error during the installation process. Any ideas?
* installing *source* package ‘Rglpk’ ...
** package ‘Rglpk’ successfully unpacked and MD5 sums checked
** libs
/bin/sh: line 0: cd: GLPK: No such file or directory
make: *** [GLPK.ts] Error 1
ERROR: compilation failed for package ‘Rglpk’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/Rglpk’
ERROR: dependency ‘Rglpk’ is not available for package ‘sparkTable’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/sparkTable’
sudo apt-get install libglpk-dev
did the trick for me.
I had this problem and took a good bit of digging in the package to understand what was happening. If Rgplk can't compile its test program when installing, it does something weird, including this bizarre cd to nowhere. Assuming glpk-devel is installed, the reason it can't compile the test program is that it can't find the gplk header as it is in a non-standard directory.
Just set the environment variable CPATH=/usr/include/glpk
and the test program will compile, allowing the package install to proceed normally.
I had this problem too. The following steps solved this issue for me. My current setup:
OS: Scientifc Linux version 6.5 (on a High Performance Cluster Server)
local user, no root access.
GLPK was not installed
Install GLPK in a local directory:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=/home/<username>/GLPK
make
make install
Install Rglpk (0.6-3):
cd ~
wget http://cran.r-project.org/src/contrib/Rglpk_0.6-3.tar.gz
export LIBRARY_PATH=/home/<username>/GLPK/lib
R CMD INSTALL Rglpk_0.6-3.tar.gz
I landed on this page, because I could not update igraph under Windows 10/11, since igraph also requires glpk as per OP. Specifically:
igraph_glpk_support.h:36:10: fatal error: glpk.h: No such file or
directory #include <glpk.h>
^~~~~~~~ compilation terminated. make: *** [C:/PROGRA~1/R/R-4.1.1/etc/x64/Makeconf:238: feedback_arc_set.o] Error
1 ERROR: compilation failed for package 'igraph'
removing 'C:/Users/xxx/Documents/R/win-library/4.1/igraph'
restoring previous 'C:/Users/xxx/Documents/R/win-library/4.1/igraph' Warning
in install.packages : installation of package ‘igraph’ had non-zero
exit status
I am under Windows 11 (but would be same for Windows 10).
Simple resolution is suggested here:
start Rtools Bash (found in all apps, Rtools 4.0 in the Windows menu)
Run pacman -S mingw-w64-x86_64-glpk and confirm with yes (y)
Run pacman -S mingw-w64-x86_64-libxml2 and confirm with yes (y)
Updating igraph in Rstudio now leads to a clean
DONE (igraph)
(there is no need to install anything, add any path, etc... just the above 4 steps)
In ubuntu 14.04, all above doesn't work. the following however works, without the need of installing libglpk-dev using apt-get.
download the glpk package from gnu and extract it:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.55.tar.gz
tar xvf glpk-4.55.tar.gz
make a GLPK directory in your local path:
mkdir ~/GLPK
configure within glpk:
cd glpk-4.55
./configure --prefix=$HOME/GLPK
cd ..
export LD_LIBRARY_PATH=$HOME/GLPK/lib
export LIBRARY_PATH=$HOME/GLPK/lib
export CPATH=$HOME/GLPK/include
download the Rglpk package from cran and extract it:
wget http://cran.r-project.org/src/contrib/Rglpk_0.6-0.tar.gz
tar xvf Rglpk_0.6_0.tar.gz
move the glpk directory into Rglpk/src and rename it to GLPK:
mv glpk-4.55 Rglpk/src/GLPK
now you can install:
R CMD INSTALL Rglpk
now a bit of explanation of what's going on. The "src/Makevars.in" file in the Rglpk package contains a line of code to enter a non-existing directory 'GLPK' within the src/ folder:
(line 11 of Makevars.in)
GLPK.ts:
#(cd GLPK && make)
touch $#
this is where the problem arises. obviously the code is trying to build glpk within that directory for some unknown reasons. and the solution above is achieved simply by moving the downloaded (and configured) glpk directory there...
If you're on a Debian-based Linux distribution, run this to install GLTK:
sudo apt install libglpk-dev
If you're on MacOS, run this to install GLTK:
brew install gltk
Finally, install the R library:
install.packages("Rglpk")
On Centos, have sudo rights. None of the above worked, but had to install GLPK in /usr/local as suggested in this SO answer. Been trying to install it for about 3 hours fml
You must install glpk dependency first.
On macOS (via homebrew):
brew install glpk
or in RStudio (via homebrew):
system("brew install glpk")
It worked for me when I combined the answers from Simón Ramírez Amaya and shadowleaves:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=$HOME/GLPK
make
make install
cd ..
export LD_LIBRARY_PATH=$HOME/GLPK/lib
export LIBRARY_PATH=$HOME/GLPK/lib
export CPATH=$HOME/GLPK/include
wget https://cran.r-project.org/src/contrib/Rglpk_0.6-4.tar.gz
R CMD INSTALL Rglpk_0.6-4.tar.gz
To load the library
dyn.load(file.path(Sys.getenv("HOME"), "GLPK", "lib", "libglpk.so"))
library(Rglpk)
The answer of Zhiying Cui is right, however, if your script has some special codes, such as foreach for parallel computing, it may raise an error.
A better way is as fellow
If your os is Centos, try
yum install glpk-devel
then just go to R or Rstudio server and
install.packages("Rglpk")
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.