Re: [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  a écrit :
> 
> 
> On 17 May 2017 at 08:46, Vaidotas Zemlys wrote:
> | Hi,
> | 
> | > Le 17 mai 2017 à 00:42, Dirk Eddelbuettel  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-base3.3.3-1~jessiecran.0  all 
>   GNU R statistical computation and graphics system
> | > | ii  openjdk-7-jre:amd647u121-2.6.8-2~deb8u1 
>   amd64OpenJDK Java runtime, using Hotspot JIT
> | > | ii  openjdk-7-jre-headless:amd64   7u121-2.6.8-2~deb8u1 
>   amd64OpenJDK 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

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

[Dirk Eddelbuettel]

On 17 May 2017 at 08:46, Vaidotas Zemlys wrote:
| Hi,
| 
| > Le 17 mai 2017 à 00:42, Dirk Eddelbuettel  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-base3.3.3-1~jessiecran.0  all   
GNU R statistical computation and graphics system
| > | ii  openjdk-7-jre:amd647u121-2.6.8-2~deb8u1   
amd64OpenJDK Java runtime, using Hotspot JIT
| > | ii  openjdk-7-jre-headless:amd64   7u121-2.6.8-2~deb8u1   
amd64OpenJDK 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.

Dirk

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

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