Cannot Run On The Command Line
On Thu, 21 Apr 2016 08:23:32 +0000
Martyn Plummer <plummerm at iarc.fr> wrote:
From: Martyn Plummer <plummerm at iarc.fr> To: "cireyapmin at gmail.com" <cireyapmin at gmail.com>, "r-sig-fedora at r-project.org" <r-sig-fedora at r-project.org> Subject: Re: [R-sig-Fedora] Cannot Run On The Command Line Date: Thu, 21 Apr 2016 08:23:32 +0000 Virgo, That message from "Ellen" is obviously spam and most likely a phishing attempt. As list administrator there is nothing I can do about it since they are not subscribed under that email address.
Thanks Martyn! I hesitated to ignore it in case "Ellen K" (see <https://en.wikipedia.org/wiki/Ellen_K>) were hilariously mocking my message be addressed at the wrong place.
Anyway, to address your question I am on FC23 and have no problem with the java JDK available from the Fedora repository (Current version 1.8.0_77). I suggest you use that and not the Oracle one.
So, I just tried to switch back to OpenJDK for the sake of testing, at no avail. # alternatives --config java There are 2 programs which provide 'java'. Selection Command ----------------------------------------------- * 1 /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64/jre/bin/java + 2 /usr/java/jdk1.8.0_92/jre/bin/java Enter to keep the current selection[+], or type selection number: 1 # alternatives --config javac There are 2 programs which provide 'javac'. Selection Command ----------------------------------------------- + 1 /usr/java/jdk1.8.0_92/bin/javac * 2 /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64/bin/javac Enter to keep the current selection[+], or type selection number: 2 # java -version openjdk version "1.8.0_77" OpenJDK Runtime Environment (build 1.8.0_77-b03) OpenJDK 64-Bit Server VM (build 25.77-b03, mixed mode) # printf "%s\n" "$JAVA" "$JAVA_HOME" "$JAVAC" "$JAVAH" "$JAR" /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64/bin/java /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64 /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64/bin/javac /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64/bin/javah /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64/bin/jar # R CMD javareconf ... JAVA_HOME : /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-1.b03.fc23.x86_64 Java library path: $(JAVA_HOME)/jre/lib/amd64/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm Updating Java configuration in /usr/lib64/R Done. # R --quiet
$ java -version openjdk version "1.8.0_77" OpenJDK Runtime Environment (build 1.8.0_77-b03) OpenJDK 64-Bit Server VM (build 25.77-b03, mixed mode) $ R --quiet /usr/bin/R: line 238: /usr/lib64/R/etc/ldpaths: Permission denied The JDK is not the culprit here, and I'm at lost right now since I can't see where else to try nailing down the error. What kinf of logs should I provide to make the issue reproducible?
Martyn On Thu, 2016-04-21 at 07:48 +0100, virgo wrote:
On Wed, 20 Apr 2016 20:50:57 +0000 "Ellen K" <keyes at pushyes.xyz> wrote:
<spam deleted>
Hi Ellen, Yes, I may be on the wrong list, could you please give a pointer to the right one? By the way, I've looked further for the culprit and it turned out that SELinux had nothing to do with the error. It rather occurs after a Java Development Kit update followed by? $ sudo R CMD javareconf The JDK is the Oracle's. $ java -version java version "1.8.0_92" Java(TM) SE Runtime Environment (build 1.8.0_92-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.92-b14, mixed mode) Maybe I should take this to Fedora's mailing lists, but so far only R is having trouble and I thought here would be the right place to seek for some help.