So nearly there, but can't install rJava

From: "Sebastian Meyer" <seb.meyer at fau.de> 
To: "r-sig-debian" <r-sig-debian at r-project.org> 
Sent: Tuesday, 22 January, 2019 15:22:33 
Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava 

Dear Chris, 

Maybe you could try debugging the error 

*** Java interpreter doesn't work properly. 

based on the underlying javareconf script. 

Scrolling through 

less `R RHOME`/bin/javareconf 

we can see that the script exits from 

echo "Java interpreter : $JAVA" 
jires=`$JAVA -classpath ${tools_classpath} getsp -test` 
if test "$jires" != "Test1234OK"; then 
echo "$jires" 
echo "~*** Java interpreter doesn't work properly.~"|${SED-sed} -e 'y/~/\n/' >&2 
exit 1 
fi 

From your output we can see that the Java interpreter ($JAVA) has been 
found at /usr/lib/jvm/default-java/jre/bin/java, but the subsequent call 
failed / didn't return the expected test result. 

You could try to run that code manually and see what you get and where 
the problem is: 

JAVA=`R CMD config JAVA` 
echo $JAVA 
## /usr/lib/jvm/default-java/jre/bin/java 

R_SHARE_DIR=`R --slave -e 'cat(R.home("share"))'` 
echo $R_SHARE_DIR 
## /usr/share/R/share 

tools_classpath=${R_SHARE_DIR}/java 
ls $tools_classpath 
## getsp.class README 

$JAVA -classpath ${tools_classpath} getsp -test 
## Test1234OK 

NB: the variable R_SHARE_DIR is set in the `which R` script. 

Good luck! 

Sebastian 


Am 22.01.19 um 14:45 schrieb Chris Evans: 

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 into quite a lot of manual 
identification of dependencies and I worked through all the ones I hit until I 
was left with the only packages I use that I can't 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' 
compiler : '/usr/lib/jvm/default-java/bin/javac' 
header prep.: '/usr/lib/jvm/default-java/bin/javah' 
cpp flags : '' 
java libs : '' 
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. 

If you don't have root privileges, run 
R CMD javareconf -e 
to set all Java-related variables and then install rJava. 

ERROR: configuration failed for package ?rJava? 
* removing ?/usr/local/lib/R/site-library/rJava? 

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/") 
options("java.home") 

$java.home 
[1] "/usr/lib/jvm/java-8-openjdk-amd64/" 

but that doesn't change things. 

As far as I can see Debian is happy with the setup of java and javac: 

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# java -version 
openjdk version "1.8.0_181" 
OpenJDK Runtime Environment (build 1.8.0_181-8u181-b13-2~deb9u1-b13) 
OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode) 
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# javac -version 
javac 1.8.0_181 
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives --config 
javac 
There is only one alternative in link group javac (providing /usr/bin/javac): 
/usr/lib/jvm/java-8-openjdk-amd64/bin/javac 
Nothing to configure. 
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives --config 
java 
There is only one alternative in link group java (providing /usr/bin/java): 
/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java 
Nothing to configure. 
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 

And I have the full jdk not just the headless version I can see the header 
files: 

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# ls -lsart 
/usr/lib/jvm/java-8-openjdk-amd64/include/ 
total 220 
80 -rw-r--r-- 1 root root 78425 Oct 22 19:05 jvmti.h 
8 -rw-r--r-- 1 root root 4771 Oct 22 19:05 jvmticmlr.h 
76 -rw-r--r-- 1 root root 74698 Oct 22 19:05 jni.h 
8 -rw-r--r-- 1 root root 7404 Oct 22 19:05 jdwpTransport.h 
12 -rw-r--r-- 1 root root 9687 Oct 22 19:05 jawt.h 
24 -rw-r--r-- 1 root root 21125 Oct 22 19:05 classfile_constants.h 
4 drwxr-xr-x 2 root root 4096 Jan 22 08:09 linux 
4 drwxr-xr-x 3 root root 4096 Jan 22 08:09 . 
4 drwxr-xr-x 8 root root 4096 Jan 22 12:55 .. 
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 

But I can't reconfigure R for Java: 

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf 
*** JAVA_HOME is not a valid path, ignoring 
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java 
/usr/lib/R/bin/javareconf: 1: /usr/lib/R/bin/javareconf: 
/usr/lib/jvm/default-java/jre/bin/java: not found 


*** Java interpreter doesn't work properly. 

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 

I hope this helps someone see something I can fix! 

Tangential question: surely I'm not rare in running R 3.5.2 on Stretch am I? 
Other tangential question: is there anything that can be done to fix the 
r-api-3/r-api-3.5 issue. You can see I'm no programmer or sysadmin but if 
there is anything I can do to help ...? 

TIA all, 

Chris 



----- Original Message ----- 

From: "Dirk Eddelbuettel" <edd at debian.org> 
To: "Chris Evans" <chrishold at psyctc.org> 
Cc: "r-sig-debian" <r-sig-debian at r-project.org> 
Sent: Tuesday, 22 January, 2019 12:21:39 
Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava 

On 22 January 2019 at 10:14, Chris Evans wrote: 
| root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get install 
| openjdk-8-jdk-headless 
| Reading package lists... Done 
| Building dependency tree 
| Reading state information... Done 
| openjdk-8-jdk-headless is already the newest version (8u181-b13-2~deb9u1). 
| openjdk-8-jdk-headless set to manually installed. 
| 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 
| 
| Anyone else got any ideas? 

Install the full-blown jdk no just headless. 

In the sources for rJava I have as a build-depends 

openjdk-10-jdk 

which may of course be a virtual. At some point we had more than JDK 
implementation. See what you can find there. 

Dirk 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org