[R-sig-Fedora] Cannot Run On The Command Line

[virgo]

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.