R SIG Debian - May 2017 - r-cran-rjava dependencies on debian jesse, library(rJava) fails when default-jre is missing

Hi,
> Le 17 mai 2017 ? 00:42, Dirk Eddelbuettel <edd at debian.org> a ?crit
:
> 
> 
> 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.

Vaidotas Zemlys-Balevi?ius

On 17 May 2017 at 08:46, Vaidotas Zemlys wrote:
| Hi,
| 
| > Le 17 mai 2017 ? 00:42, Dirk Eddelbuettel <edd at debian.org> a
?crit :
| > 
| > 
| > 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.

Dirk

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

Hi,
> Le 17 mai 2017 ? 13:54, Dirk Eddelbuettel <edd at debian.org> a ?crit
:
> 
> 
> On 17 May 2017 at 08:46, Vaidotas Zemlys wrote:
> | Hi,
> | 
> | > Le 17 mai 2017 ? 00:42, Dirk Eddelbuettel <edd at debian.org>
a ?crit :
> | > 
> | > 
> | > 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-Balevi?ius