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Chris Evans

2019-Jan-22 13:45 UTC

[R-sig-Debian] So nearly there, but can't install rJava

Thanks Dirk and Enrico,

First clarification: I'm in this mess because I'm trying to run R 3.5.2
within Debian stable (9/"sretch") using the stretch-cran35 repository.
That uses and provides r-api-35 but many of the packages depend upon r-api-3. 
As Johannes said a day or so back, the way around this is to use
install.packages() in R to get the packages you want. That leads you into quite
a lot of manual identification of dependencies and I worked through all the ones
I hit until I was left with the only packages I use that I can't install
sharing just one dependency: they all depend on rJava and I can't install
from the r-cran-rjava package in the stretch-cran35 repository because
that's one of the packages that depends on r-api-3.

I thought that installing the default java and jdk Debian packages and using R
CMD javareconf (as root) would set the right variables for
install.packages("rJava") to work but no go.  It fails with this
information:

checking Java support in R... present:
interpreter : '/usr/lib/jvm/default-java/jre/bin/java'
archiver    : '/usr/lib/jvm/default-java/bin/jar'
compiler    : '/usr/lib/jvm/default-java/bin/javac'
header prep.: '/usr/lib/jvm/default-java/bin/javah'
cpp flags   : ''
java libs   : ''
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.

If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.

ERROR: configuration failed for package ?rJava?
* removing ?/usr/local/lib/R/site-library/rJava?

I think the problem may be options setting where R/rJava will look for Java so I
tried:
> options(java.home="/usr/lib/jvm/java-8-openjdk-amd64/")
> options("java.home")$java.home
[1] "/usr/lib/jvm/java-8-openjdk-amd64/"

but that doesn't change things. 

As far as I can see Debian is happy with the setup of java and javac:

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# java -version
openjdk version "1.8.0_181"
OpenJDK Runtime Environment (build 1.8.0_181-8u181-b13-2~deb9u1-b13)
OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode)
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# javac -version
javac 1.8.0_181
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives
--config javac
There is only one alternative in link group javac (providing /usr/bin/javac):
/usr/lib/jvm/java-8-openjdk-amd64/bin/javac
Nothing to configure.
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives
--config java
There is only one alternative in link group java (providing /usr/bin/java):
/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
Nothing to configure.
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 

And I have the full jdk not just the headless version I can see the header
files:

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# ls -lsart
/usr/lib/jvm/java-8-openjdk-amd64/include/
total 220
80 -rw-r--r-- 1 root root 78425 Oct 22 19:05 jvmti.h
 8 -rw-r--r-- 1 root root  4771 Oct 22 19:05 jvmticmlr.h
76 -rw-r--r-- 1 root root 74698 Oct 22 19:05 jni.h
 8 -rw-r--r-- 1 root root  7404 Oct 22 19:05 jdwpTransport.h
12 -rw-r--r-- 1 root root  9687 Oct 22 19:05 jawt.h
24 -rw-r--r-- 1 root root 21125 Oct 22 19:05 classfile_constants.h
 4 drwxr-xr-x 2 root root  4096 Jan 22 08:09 linux
 4 drwxr-xr-x 3 root root  4096 Jan 22 08:09 .
 4 drwxr-xr-x 8 root root  4096 Jan 22 12:55 ..
root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 

But I can't reconfigure R for Java:

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
/usr/lib/R/bin/javareconf: 1: /usr/lib/R/bin/javareconf:
/usr/lib/jvm/default-java/jre/bin/java: not found

*** Java interpreter doesn't work properly.

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 

I hope this helps someone see something I can fix!

Tangential question: surely I'm not rare in running R 3.5.2 on Stretch am I?
Other tangential question: is there anything that can be done to fix the
r-api-3/r-api-3.5 issue.  You can see I'm no programmer or sysadmin but if
there is anything I can do to help ...?

TIA all,

Chris

----- Original Message -----> From: "Dirk Eddelbuettel" <edd at debian.org>
> To: "Chris Evans" <chrishold at psyctc.org>
> Cc: "r-sig-debian" <r-sig-debian at r-project.org>
> Sent: Tuesday, 22 January, 2019 12:21:39
> Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava
> On 22 January 2019 at 10:14, Chris Evans wrote:
>| root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get install
>| openjdk-8-jdk-headless
>| Reading package lists... Done
>| Building dependency tree
>| Reading state information... Done
>| openjdk-8-jdk-headless is already the newest version (8u181-b13-2~deb9u1).
>| openjdk-8-jdk-headless set to manually installed.
>| 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
>| 
>| Anyone else got any ideas?
> 
> Install the full-blown jdk no just headless.
> 
> In the sources for rJava I have as a build-depends
> 
>   openjdk-10-jdk
> 
> which may of course be a virtual. At some point we had more than JDK
> implementation.  See what you can find there.
> 
> Dirk
> 
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
-- 
Chris Evans <chris at psyctc.org> Skype: chris-psyctc
Visiting Professor, University of Sheffield <chris.evans at
sheffield.ac.uk>
I do some consultation work for the University of Roehampton <chris.evans at
roehampton.ac.uk> and other places but this <chris at psyctc.org>
remains my main Email address.
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book
to talk, I am trying to keep that to Thursdays and my diary is now available at:
https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/
Beware: French time, generally an hour ahead of UK.  That page will also take
you to my blog which started with earlier joys in France and Spain!

Johannes Ranke

2019-Jan-22 14:18 UTC

head link

[R-sig-Debian] So nearly there, but can't install rJava

Hi Chris,
> I think the problem may be options setting where R/rJava will look for Java
so I tried:> > options(java.home="/usr/lib/jvm/java-8-openjdk-amd64/")
This should not be necessary. I would recommend to start a fresh R session in 
order to unset this.
> As far as I can see Debian is happy with the setup of java and javac:
> ...
> And I have the full jdk not just the headless version I can see the header
> files:
> ...
> But I can't reconfigure R for Java:
> 
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf
> *** JAVA_HOME is not a valid path, ignoring
as above, I would not recommend setting JAVA_HOME manually.
> Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
> /usr/lib/R/bin/javareconf: 1: /usr/lib/R/bin/javareconf:
> /usr/lib/jvm/default-java/jre/bin/java: not found
Obviously this file was not found. Again, apt-file can provide some help (but 
not when giving it the full path, because of the link maintained by update-
alternatives:

  apt-file search jre/bin/java

If you have openjdk-8-jre-headless installed, this file should be there on your 
system. Seems you don't have the jre installed?

...
> Tangential question: surely I'm not rare in running R 3.5.2 on Stretch
am I?
I for sure am running it without issues on several computers. On my desktop, I 
am using openjdk-9 from stretch-backports, but on my laptop I just upgraded 
from R 3.4.x to R 3.5.2 using the stretch-cran35 packages on CRAN, and had no 
issues. I could install rJava from within R, and after that R CMD javareconf 
gives me:

Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
Java version     : 1.8.0_181
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/lib/jvm/default-java/bin/javah
Java archive tool: /usr/lib/jvm/default-java/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/default-java/
include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-
prefix-map=/home/jranke/git/r-backports/stretch/r-base-3.4.3=. -fstack-
protector-strong -Wformat -Werror=format-security -Wdate-time -
D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o conftest.so conftest.o 
-L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.
> Other tangential question: is there anything that can be done to fix the
> r-api-3/r-api-3.5 issue.  You can see I'm no programmer or sysadmin but
if
> there is anything I can do to help ...?
Thanks for the offer. Personally, I am always glad to get some feedback from 
people using the Debian backports on CRAN, so thanks for that. On the other 
hand, I do not think that there is an error to be fixed. Of course it would be 
nice if we could provide more precompiled debs for these backports in order to 
avoid having to install them from sources. For me personally, this is not a 
priority, I am happy if I manage to get the base and recommended packages out 
on new releases.

Johannes
> 
> TIA all,
> 
> Chris
> 
> 
> 
> ----- Original Message -----
> 
> > From: "Dirk Eddelbuettel" <edd at debian.org>
> > To: "Chris Evans" <chrishold at psyctc.org>
> > Cc: "r-sig-debian" <r-sig-debian at r-project.org>
> > Sent: Tuesday, 22 January, 2019 12:21:39
> > Subject: Re: [R-sig-Debian] So nearly there, but can't install
rJava
> > 
> > On 22 January 2019 at 10:14, Chris Evans wrote:
> >| root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get install
> >| openjdk-8-jdk-headless
> >| Reading package lists... Done
> >| Building dependency tree
> >| Reading state information... Done
> >| openjdk-8-jdk-headless is already the newest version
> >| (8u181-b13-2~deb9u1).
> >| openjdk-8-jdk-headless set to manually installed.
> >| 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> >| 
> >| Anyone else got any ideas?
> > 
> > Install the full-blown jdk no just headless.
> > 
> > In the sources for rJava I have as a build-depends
> > 
> >   openjdk-10-jdk
> > 
> > which may of course be a virtual. At some point we had more than JDK
> > implementation.  See what you can find there.
> > 
> > Dirk
> > 
> > --
> > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

-- 
Johannes Ranke
Wissenschaftlicher Berater
https://jrwb.de/contact

Dirk Eddelbuettel

2019-Jan-22 15:05 UTC

head link

[R-sig-Debian] So nearly there, but can't install rJava

On 22 January 2019 at 15:18, Johannes Ranke wrote:
| Thanks for the offer. Personally, I am always glad to get some feedback from 
| people using the Debian backports on CRAN, so thanks for that. On the other 
| hand, I do not think that there is an error to be fixed. Of course it would be
| nice if we could provide more precompiled debs for these backports in order to
| avoid having to install them from sources. For me personally, this is not a 
| priority, I am happy if I manage to get the base and recommended packages out 
| on new releases.

Right.

And for what it is worth we do have several working choices -- and eg the
Ubuntu side has over 4000 r-cran-* binary packages for the LTS releases (ie
Ubuntu's variant of stable).  Debian testing has fewer, but it a little more
current on other things. And one can always mix and match binary
installations and from CRAN installation.  Most users should find their
preferred way among these choices.

It should be said, though, that Chris did chose what at least to me appears
to be the most constrained choice.

Dirk

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

Sebastian Meyer

2019-Jan-22 15:22 UTC

head link

[R-sig-Debian] So nearly there, but can't install rJava

Dear Chris,

Maybe you could try debugging the error
> *** Java interpreter doesn't work properly.
based on the underlying javareconf script.

Scrolling through
> less `R RHOME`/bin/javareconf
we can see that the script exits from
> echo "Java interpreter : $JAVA"
> jires=`$JAVA -classpath ${tools_classpath} getsp -test`
> if test "$jires" != "Test1234OK"; then
>     echo "$jires"
>     echo "~*** Java interpreter doesn't work
properly.~"|${SED-sed} -e 'y/~/\n/' >&2
>     exit 1
> fi
>From your output we can see that the Java interpreter ($JAVA) has beenfound at /usr/lib/jvm/default-java/jre/bin/java, but the subsequent call
failed / didn't return the expected test result.

You could try to run that code manually and see what you get and where
the problem is:
> JAVA=`R CMD config JAVA`
> echo $JAVA
> ## /usr/lib/jvm/default-java/jre/bin/java
> R_SHARE_DIR=`R --slave -e 'cat(R.home("share"))'`
> echo $R_SHARE_DIR
> ## /usr/share/R/share
> tools_classpath=${R_SHARE_DIR}/java
> ls $tools_classpath
> ## getsp.class  README
> $JAVA -classpath ${tools_classpath} getsp -test
> ## Test1234OK
NB: the variable R_SHARE_DIR is set in the `which R` script.

Good luck!

	Sebastian


Am 22.01.19 um 14:45 schrieb Chris Evans:> Thanks Dirk and Enrico,
> 
> First clarification: I'm in this mess because I'm trying to run R
3.5.2 within Debian stable (9/"sretch") using the stretch-cran35
repository. That uses and provides r-api-35 but many of the packages depend upon
r-api-3.  As Johannes said a day or so back, the way around this is to use
install.packages() in R to get the packages you want. That leads you into quite
a lot of manual identification of dependencies and I worked through all the ones
I hit until I was left with the only packages I use that I can't install
sharing just one dependency: they all depend on rJava and I can't install
from the r-cran-rjava package in the stretch-cran35 repository because
that's one of the packages that depends on r-api-3.
> 
> I thought that installing the default java and jdk Debian packages and
using R CMD javareconf (as root) would set the right variables for
install.packages("rJava") to work but no go.  It fails with this
information:
> 
> checking Java support in R... present:
> interpreter : '/usr/lib/jvm/default-java/jre/bin/java'
> archiver    : '/usr/lib/jvm/default-java/bin/jar'
> compiler    : '/usr/lib/jvm/default-java/bin/javac'
> header prep.: '/usr/lib/jvm/default-java/bin/javah'
> cpp flags   : ''
> java libs   : ''
> configure: error: One or more Java configuration variables are not set.
> Make sure R is configured with full Java support (including JDK). Run
> R CMD javareconf
> as root to add Java support to R.
> 
> If you don't have root privileges, run
> R CMD javareconf -e
> to set all Java-related variables and then install rJava.
> 
> ERROR: configuration failed for package ?rJava?
> * removing ?/usr/local/lib/R/site-library/rJava?
> 
> I think the problem may be options setting where R/rJava will look for Java
so I tried:
> 
>> options(java.home="/usr/lib/jvm/java-8-openjdk-amd64/")
>> options("java.home")
> $java.home
> [1] "/usr/lib/jvm/java-8-openjdk-amd64/"
> 
> but that doesn't change things. 
> 
> As far as I can see Debian is happy with the setup of java and javac:
> 
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# java -version
> openjdk version "1.8.0_181"
> OpenJDK Runtime Environment (build 1.8.0_181-8u181-b13-2~deb9u1-b13)
> OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode)
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# javac -version
> javac 1.8.0_181
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives
--config javac
> There is only one alternative in link group javac (providing
/usr/bin/javac): /usr/lib/jvm/java-8-openjdk-amd64/bin/javac
> Nothing to configure.
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives
--config java
> There is only one alternative in link group java (providing /usr/bin/java):
/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
> Nothing to configure.
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 
> 
> And I have the full jdk not just the headless version I can see the header
files:
> 
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# ls -lsart
/usr/lib/jvm/java-8-openjdk-amd64/include/
> total 220
> 80 -rw-r--r-- 1 root root 78425 Oct 22 19:05 jvmti.h
>  8 -rw-r--r-- 1 root root  4771 Oct 22 19:05 jvmticmlr.h
> 76 -rw-r--r-- 1 root root 74698 Oct 22 19:05 jni.h
>  8 -rw-r--r-- 1 root root  7404 Oct 22 19:05 jdwpTransport.h
> 12 -rw-r--r-- 1 root root  9687 Oct 22 19:05 jawt.h
> 24 -rw-r--r-- 1 root root 21125 Oct 22 19:05 classfile_constants.h
>  4 drwxr-xr-x 2 root root  4096 Jan 22 08:09 linux
>  4 drwxr-xr-x 3 root root  4096 Jan 22 08:09 .
>  4 drwxr-xr-x 8 root root  4096 Jan 22 12:55 ..
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 
> 
> But I can't reconfigure R for Java:
> 
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf
> *** JAVA_HOME is not a valid path, ignoring
> Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
> /usr/lib/R/bin/javareconf: 1: /usr/lib/R/bin/javareconf:
/usr/lib/jvm/default-java/jre/bin/java: not found
> 
> 
> *** Java interpreter doesn't work properly.
> 
> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# 
> 
> I hope this helps someone see something I can fix!
> 
> Tangential question: surely I'm not rare in running R 3.5.2 on Stretch
am I?
> Other tangential question: is there anything that can be done to fix the
r-api-3/r-api-3.5 issue.  You can see I'm no programmer or sysadmin but if
there is anything I can do to help ...?
> 
> TIA all,
> 
> Chris
> 
> 
> 
> ----- Original Message -----
>> From: "Dirk Eddelbuettel" <edd at debian.org>
>> To: "Chris Evans" <chrishold at psyctc.org>
>> Cc: "r-sig-debian" <r-sig-debian at r-project.org>
>> Sent: Tuesday, 22 January, 2019 12:21:39
>> Subject: Re: [R-sig-Debian] So nearly there, but can't install
rJava
> 
>> On 22 January 2019 at 10:14, Chris Evans wrote:
>> | root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get install
>> | openjdk-8-jdk-headless
>> | Reading package lists... Done
>> | Building dependency tree
>> | Reading state information... Done
>> | openjdk-8-jdk-headless is already the newest version
(8u181-b13-2~deb9u1).
>> | openjdk-8-jdk-headless set to manually installed.
>> | 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
>> | 
>> | Anyone else got any ideas?
>>
>> Install the full-blown jdk no just headless.
>>
>> In the sources for rJava I have as a build-depends
>>
>>   openjdk-10-jdk
>>
>> which may of course be a virtual. At some point we had more than JDK
>> implementation.  See what you can find there.
>>
>> Dirk
>>
>> --
>> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>

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