similar to: Going in circles

Morning All: Having problems installing this one into my R setup and wondered if anyone on the list had the same problem and found a workable solution. First to the system particulars: OS is the Hardy Heron edition of Ubuntu Linux R version is 2.13.1 Java installation is sun-java6 Next up is the result of javareconf: R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.5.0

Dear all, Installing rJava fails. The message was listed below. I wonder why cpp flag could not be detected, although I had installed. Thanks!!! -Jiacheng R CMD INSTALL rJava_0.9-0.tar.gz * installing to library ‘/data1/mri_researchers/wexler_data/jiacheng/R-2.12.0/library’ * installing *source* package ‘rJava’ ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file

Morning All: Having problems installing this one into my R setup and wondered if anyone on the list had the same problem and found a workable solution. First to the system particulars: OS is the Hardy Heron edition of Ubuntu Linux R version is 2.13.1 Java installation is sun-java6 Next up is the result of javareconf: R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.5.0

Hi Ista! Thanks a lot for your support!! It puzzles me because it?s the first time that something like this happens to me. I?m aware that root and user don?t have the same environmental variables here. However, I don?t know why root chooses Java 9 and my user chooses Java 10. Isn?t Java 10 ready to be used as a root? It seems that we are going to have to wait until rJava releases a new

Hi Jeff!! I really don?t know if running R CMD javareconf with sudo has posed a problem here, now or in the past. What I know is sometimes it?s the only way to really config it, if I don?t run with sudo, in the end it asks me if I want to overwrite the configuration from root override rw-r--r-- root/admin for /usr/local/Cellar/r/3.4.4/lib/R/etc/Makeconf? (y/n [n]) y override rw-r--r--

Thanks Sebastian, Johannes and Dirk for your inputs, I think this can be marked [SOLVED] though I still don't understand how it started. The answer seems to be that something sets an environment variable JAVA.LIBRARY.PATH and this wasn't set correctly. I had never directly done anything to set that so that's odd but what I had done that was causing the problem (I think) is that I had

I am not a Mac user, but I do use Linux and I would recommend not running R with sudo unless you are an admin ninja. That defensive practice would render the answer to your question moot. It is possible that your problem may have started with inappropriate use of sudo in configuring java, but configuring Java is not on-topic here. -- Sent from my phone. Please excuse my brevity. On March 27,

Hi Chris, > I think the problem may be options setting where R/rJava will look for Java so I tried: > > options(java.home="/usr/lib/jvm/java-8-openjdk-amd64/") This should not be necessary. I would recommend to start a fresh R session in order to unset this. > As far as I can see Debian is happy with the setup of java and javac: > ... > And I have the full jdk

Hi! I?m on macOS 10.13.3 and just installed the new Java 10 using Homebrew Cask. I also have installed R with Homebrew. Everything seems to work fine, however I just get different outputs if I run sudo R CMD javareconf or R CMD javareconf. With sudo I get pointed to Java 9 and without sudo I get pointed to Java 10. I really don?t know why. Without sudo: $ R CMD javareconf

Thanks Dirk and Enrico, First clarification: I'm in this mess because I'm trying to run R 3.5.2 within Debian stable (9/"sretch") using the stretch-cran35 repository. That uses and provides r-api-35 but many of the packages depend upon r-api-3. As Johannes said a day or so back, the way around this is to use install.packages() in R to get the packages you want. That leads you

Hi I'm a problem with installing "rJava" in Linux I have got in my system : java-sun, java-sun-tools, java-sun-jre but if I wont install rJava I got a problem like this: > install.packages("rJava", dependencies = TRUE) --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.mirroring.de/src/contrib/rJava_0.8-2.tar.gz' Content type

attempting to install rJava on R-2.7.0, x86_64 platform, config.log shows the following error: configure:3880: checking whether JNI programs can be compiled configure:3898: gcc -m64 -std=gnu99 -o conftest -g -O2 -I/path/to/x86-64-linux/jdk-1.6.0_06/jre/../include conftest.c -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64/server -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64

Hello, I am running: R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 on a 64-bit RedHat box. To encourage collegues to use R, I am trying to install "JGR", which depends on "rJava", on the above machine. At first I received and error saying Java was not available. My IT support, I am not admin. on this

Esteemed useRs and Devs, Attempts to update package:rJava to the latest version have failed. See my code and output below. Notably, as suggested here http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing $ sudo apt-get install r-cran-rjava ran successfully without error or warning, but my rJava package is not updated, and remains un-updatable... Greatly appreciate any

Hi, I was trying install rJava package but failed to install with below error: *trying URL 'https://cloud.r-project.org/src/contrib/rJava_0.9-11.tar.gz <https://cloud.r-project.org/src/contrib/rJava_0.9-11.tar.gz>'* *Content type 'application/x-gzip' length 675188 bytes (659 KB)* *==================================================* *downloaded 659 KB* ** installing

I encountered some failures in using install.packages() to install rgl and rJava in some of my (multiple) Ubuntu Hardy systems. A quick search of the 'Net did not show any debian packages for these. The install.packages messages said header or other files were missing, suggesting path and related woes. Email with Duncan Murdoch (thanks!) pointed the way with rgl and led to a fix for rJava

Installing rJava fails consistently, whether installed via the command line as below, or through "install.packages( 'rJava' )", and whether 0.84 or 0.85 is used, with the message :- "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

Dear all, I have had the same problem as stated before, even with SUN's jdk installed, and therefore enable to install any of 'iplots', 'rJava' or 'JGR' packages. It seemed however that the R CMD javareconf couldn't catch the path of my actual jdk. The following worked for me by forcing the JAVA_HOME environment variable: env

I am trying to build R on a Centos server without admin privileges (or support), so I can call R functions from NetLogo models (via the NetLogo R extension or possibly Rserve), but I'm getting stuck near the end of make. Any suggestions? Here's the setup... $ R_SHELL=/bin/sh $ R_HOME=~/R-devel $ cd $R_HOME; ./configure; make returns ... begin installing recommended package MASS

Hi, I am unable to install the package rJava. I tried doing what the output suggests, but it doesn't help. How can I get R to find/recognize my Java installation? I am running R-2.15.0. waichler at snow> sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_22 Java home path : /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre Java compiler : /usr/bin/javac Java