search for: javareconf

Full_Name: Tom Callaway Version: 2.7.2 OS: Fedora 10 (Linux/x86_64) Submission from: (NULL) (96.233.67.230) Recently, Debian identified a security issue with the javareconf script in R. I confirmed that this is still unfixed in R 2.7.2. The following patch resolves the issue: diff -up R-2.7.2/src/scripts/javareconf.BAD R-2.7.1/src/scripts/javareconf --- R-2.7.2/src/scripts/javareconf.BAD 2008-08-29 11:04:21.000000000 -0400 +++ R-2.7.2/src/scripts/javareconf 2008-08...

Hi All, Running R CMD javareconf -e (or R CMD javareconf as root I am rot on my machines) Fails. / [root at penguins1lanalt etc]# R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_30 Java home path : /usr/java/jre1.6.0_30 Java compiler : not present Java headers gen.: Java archive tool: Java libra...

Hello, I am using EC2 to launch several instances. On each instance, I perform the following commands yum -y install R (installs R-2.6) R CMD javareconf sleep 10 wget rpackage.tgz R CMD INSTALL rpackage.tgz Now, rpackage.tgz needs to be built with jni libraries. When the instance is fully up, i log in and check if rpackage was successfully installed and find out it wasn't. Running R CMD INSTALL rpackage.tgz again, i get the response that I s...

Hi, Wasn't able to see a bug report on this issue yet... Hope I'm not doublng up. There seems to be little info around for what "R CMD javareconf" does but it has some deprecation errors seemingly. On running cmd in terminal: Java interpreter : /usr/bin/java Java version : 9 Java home path : /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java arc...

...va-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' configure: error: One or more Java configuration variables are not set. Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. ## When I run R CMD javareconf as root, I get: ## # R CMD javareconf *** JAVA_HOME is not a valid path, ignoring Java interpreter : /usr/bin/java Java version : 1.6.0_0 Java home path : /usr/lib/jvm/java-6-openjdk/jre Java compiler : /usr/bin/javac Java...

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/Makecon...

...5:33 PM PDT, Luis Puerto <luiss.puerto at gmail.com> wrote: >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 > >Java interpreter : >/Library/Java/Jav...

Hi Dirk, hi list, I just ran into a slight problem while building the recommended packages for CRAN in a chroot environment against the fresh backport of your R 2.6.0 packages. It seems that R CMD javareconf wants to change files in /etc/R during the build, and since I am not building the packages as root in my etch chroot, this fails, even if I am using fakeroot. My workaround was to simply remove gij-4.1 from the chroot, so /usr/bin/java is not found any more. Johannes -- Dr. Johannes Ranke...

Hi folks: I guess my earlier posting was too involved, so let me try to get to the essence of my problem. I recently tried to compile JGR, rJava, etc. into my updated R. First, I ran: R CMD javareconf. The output from that tells me that "JAVA_HOME is not a valid path, ignoring" and the cpp flags are set to nothing. The javareconf fills most of the variables with references to openjdk. JAVA_HOME, as far as I can tell, points to a properly installed copy of Sun Java. When I run updat...

Has anyone successfully installed rJava on Debian squeeze (or any other version of linux)? I keep getting the ... (JDK) is missing or not registered in R error message when installing the package. I've tried running 'R CMD javareconf', setting JAVA_HOME and editing /etc/R/ldpaths by hand, but to no avail. The problem might be related to the R_JAVA_LD_LIBRARY_PATH that's set in /etc/R/ldpaths. Does anyone know what it's supposed to contain? I haven't been able to find any documentation on it? Searching the...

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 Java interpreter : /Library/Java/JavaVirtualMachines/jdk-10.jdk/Cont...

...4, Ista Zahn <istazahn at gmail.com <mailto:istazahn at gmail.com>> wrote: > > On Wed, Mar 28, 2018 at 3:56 AM, Luis Puerto <luiss.puerto at gmail.com <mailto:luiss.puerto at gmail.com>> wrote: >> 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...

...install sharing just one dependency: they all depend on rJava and I can't install from the r-cran-rjava package in the stretch-cran35 repository because that's one of the packages that depends on r-api-3. I thought that installing the default java and jdk Debian packages and using R CMD javareconf (as root) would set the right variables for install.packages("rJava") to work but no go. It fails with this information: checking Java support in R... present: interpreter : '/usr/lib/jvm/default-java/jre/bin/java' archiver : '/usr/lib/jvm/default-java/bin/jar' compil...

...re/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' configure: error: Java Development Kit (JDK) is missing or not registered in R Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. When I then do that > sudo R CMD javareconf # at terminal I get this: Updating Java configuration in /etc/R Done. However, it still doesn't work, returning the same crap as before. Also, when I try > R CMD javareconf -e # at terminal I just get sh...

...LC_MESSAGES=en_IE.UTF-8 [7] LC_PAPER=en_IE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base > root at SeansPC:~# R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_15 Java home path : /usr/lib/jvm/java-6-sun-1.6.0.15/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOM...

...: 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 Java home path : /usr/lib/jvm/java-1.5.0-gcj-4.2-1.5.0.0/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: /usr/lib/../lib/gcj-4.2-81:/usr/lib/jni...

Having difficulties getting rJava to install on my Debian Squeeze box. Perused the R-help list and tried some things that have worked for others but not for me. Below is the output of my attempted build, R CMD javareconf -e, and sessionInfo(). Note I tried the R CMD javareconf also as root, restarted R after each of these, all no help. * Installing *source* package ?rJava? ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes...

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 headers gen.: Java archive tool: /usr/bin/jar Java library path: $(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/...

Hi, I would like to test the new package RGG (R Gui Generator). This package requires the installation of several other package. One of them is rJava. I installed sun-java6-jdk and run the R CMD javareconf but the installation still fails ! Do you have any ideas ? * Installing *source* package ‘rJava’ ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking...

...legues 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 machine, installed Java (1.6.0_19) and JDK (1.6.0_19) and successfully ran: R CMD javareconf now, I am getting the following error: ------------------------------------------------------------------------------------------- . . . checking Java support in R... present: interpreter : '/usr/java/../bin/java' archiver : '/usr/java/../bin/jar' compiler : '/usr/java/....