On 8 May 2017 at 15:39, Vaidotas Zemlys wrote:
| Hi,
|
| Dirk Eddelbuettel advised me to write here. Here is my original letter to him:
|
| I would like to enquire about package r-cran-rjava on Debian jesse. It seems
that if default-jre package is not installed, but openjdk-7-jre is installed,
then library(rJava) in R fails. I’ve been bitten by this today and I wonder
whether this an issue of mine, or is this a possible bug.
|
| My server admin used apt-get update and apt-get upgrade today and R started
throwing an error that it cannot find libjvm.so, when trying to do
library(rJava). At first I thought that this is a problem of setting JAVA_HOME,
and setting it to JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 before starting R
seemed to solve the problem. But this setting was ignored by shiny-server, so I
spent some time figuring out how to force shiny-server to respect it. Only
after repeated failure I’ve noticed that LD_LIBRARY_PATH in Sys.getenv() points
to /usr/lib/jvm/default-java/jre/lib/amd64/server and there was no directory
/usr/lib/jvm/default-java/ in the system. Then I found out that this library is
provided by default-jre and when it was installed everything start to work.
Then I investigated further and found that this package is only optional for
r-cran-rjava. Hence the question.
|
|
| Here is my configuration:
|
| > lsb_release -a
| No LSB modules are available.
| Distributor ID: Debian
| Description: Debian GNU/Linux 8.8 (jessie)
| Release: 8.8
| Codename: jessie
|
|
| dpkg -l with relevant packages:
|
| Desired=Unknown/Install/Remove/Purge/Hold
| | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
| |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
| ||/ Name Version Architecture
Description
|
+++-=================================-=====================-=====================-========================================================================
| ii r-cran-rjava 0.9-6-3 amd64
GNU R low-level interface to Java
| ii r-base 3.3.3-1~jessiecran.0 all
GNU R statistical computation and graphics system
| ii openjdk-7-jre:amd64 7u121-2.6.8-2~deb8u1
amd64 OpenJDK Java runtime, using Hotspot JIT
| ii openjdk-7-jre-headless:amd64 7u121-2.6.8-2~deb8u1
amd64 OpenJDK Java runtime, using Hotspot JIT (headless)
|
| Sorry for bothering if this is an issue from my side.
You have the 'jre', you may need the 'jdk' for the compiler.
I think the Depends: we have is good enough for running Java based R
packages. At least it used to be...
Dirk
|
| Vaidotas Zemlys-Balevičius
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--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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