[R-sig-Debian] r-cran-rjava dependencies on debian jesse, library(rJava) fails when default-jre is missing

[Vaidotas Zemlys]

Hi,

> Le 17 mai 2017 à 13:54, Dirk Eddelbuettel <edd at debian.org> a écrit :
> 
> 
> On 17 May 2017 at 08:46, Vaidotas Zemlys wrote:
> | Hi,
> | 
> | > Le 17 mai 2017 à 00:42, Dirk Eddelbuettel <edd at debian.org> a écrit :
> | > 
> | > 
> | > 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 need the 'jdk'.
> | > 
> | 
> | But the r-cran-rjava Depends: do not mention that. Of course having packages openjdk-7-jre and openjdk-7-jdk is not at all confusing, but that is Java.
> 
> I hear you but the 'jdk' is the build-depends, and needed when you want to
> build other packages. The 'jre' is the smaller minimal set needed to only run
> code. At least that was the idea, and at some point it worked.  Maybe I need
> to enlarge the Depends to use the jdk.
> 
 
I think there is some misunderstanding. I was not able to run any R package which depended on rJava, which in binary form was provided by r-cran-rjava. The issue was that after the update the already installed R packages which were depending on rJava were not able to load. So build-depend would not have helped me, because I was not building any packages. Everything started to work after install of default-jre. Since I did not try to reproduce the bug on a clean install, there is a chance that my problem was self-inflicted, i.e. my admin did something not entirely advisable. I think we can close this issue. I’ve reported the issue, solicited the reaction and reaffirmed “java is tricky” idiom, so everything is cool from my side.


Vaidotas Zemlys-Balevičius