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

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. 

Vaidotas Zemlys-Balevi?ius

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-Balevi?ius
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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'.

Dirk

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

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