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Chris Evans

2019-Jan-22 10:14 UTC

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

As ever, I learn from this: I didn't know apt-file. Got it, installed it,
used it:

root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-file search jni.h 
android-libnativehelper-dev: /usr/include/android/nativehelper/jni.h 
android-platform-frameworks-native-headers:
/usr/include/android/android/asset_manager_jni.h
android-platform-frameworks-native-headers:
/usr/include/android/android/native_window_jni.h
gcj-6-jdk: /usr/lib/gcc/x86_64-linux-gnu/6/include/jni.h 
gcj-6-jdk: /usr/lib/jvm/java-1.5.0-gcj-6-amd64/include/jni.h 
libavcodec-dev: /usr/include/x86_64-linux-gnu/libavcodec/jni.h 
libgluegen2-build-java: /usr/share/gluegen2/make/stub_includes/jni/jni.h 
openjdk-8-jdk-headless: /usr/lib/jvm/java-8-openjdk-amd64/include/jni.h 

I was 99% sure I already had that last installed. Sure enough: 

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? 

Chris 
> From: "Johannes Ranke" <johannes.ranke at jrwb.de>
> To: "r-sig-debian" <r-sig-debian at r-project.org>,
"Chris Evans"
> <chrishold at psyctc.org>
> Sent: Tuesday, 22 January, 2019 08:47:28
> Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava
> Am Dienstag, 22. Januar 2019, 08:27:14 CET schrieb Chris Evans:
> ...
> > error: jni.h: No such file or directory
> > #include <jni.h>
> > ^
> > compilation terminated.
> You get a complaint that jni.h is missing. So one strategy would be to look
for
> this file in the available packages:
> sudo apt-file search jni.h
> One of the packages returned is openjdk-8-jdk-headless (which I happen to
have
> installed). I think (others will know for certain) that you need a Java
> Development Kit (jdk) not just a runtime environment (jre).
> Cheers,
> Johannes
-- 
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!

	[[alternative HTML version deleted]]

Dirk Eddelbuettel

2019-Jan-22 12:19 UTC

head link

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

On 22 January 2019 at 10:14, Chris Evans wrote:
| Anyone else got any ideas? 

Java can be tricky and that is one of the reasons we have r-cran-rjava
prebuilt for you. It should resolve issues and work because other binary
packages depend on it.

Otherwise, as Johannes hinted, you need a JDK if you build with rJava from
CRAN source, and 'sudo R CMD javareconf' should work.  

I don't do much work on Debian stable so no concrete tips from me.

Dirk

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

Dirk Eddelbuettel

2019-Jan-22 12:21 UTC

head link

[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

Enrico Schumann

2019-Jan-22 12:22 UTC

head link

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

>>>>> "Chris" == Chris Evans <chrishold at
psyctc.org> writes:
    Chris> As ever, I learn from this: I didn't know apt-file. Got it,
installed it, used it:
    Chris> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-file
search jni.h
    Chris> android-libnativehelper-dev:
/usr/include/android/nativehelper/jni.h
    Chris> android-platform-frameworks-native-headers:
/usr/include/android/android/asset_manager_jni.h
    Chris> android-platform-frameworks-native-headers:
/usr/include/android/android/native_window_jni.h
    Chris> gcj-6-jdk: /usr/lib/gcc/x86_64-linux-gnu/6/include/jni.h 
    Chris> gcj-6-jdk: /usr/lib/jvm/java-1.5.0-gcj-6-amd64/include/jni.h 
    Chris> libavcodec-dev: /usr/include/x86_64-linux-gnu/libavcodec/jni.h 
    Chris> libgluegen2-build-java:
/usr/share/gluegen2/make/stub_includes/jni/jni.h
    Chris> openjdk-8-jdk-headless:
/usr/lib/jvm/java-8-openjdk-amd64/include/jni.h

    Chris> I was 99% sure I already had that last installed. Sure enough: 

    Chris> root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get
install openjdk-8-jdk-headless
    Chris> Reading package lists... Done 
    Chris> Building dependency tree 
    Chris> Reading state information... Done 
    Chris> openjdk-8-jdk-headless is already the newest version
(8u181-b13-2~deb9u1).
    Chris> openjdk-8-jdk-headless set to manually installed. 
    Chris> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 

    Chris> Anyone else got any ideas? 

    Chris> Chris 

I have not followed the discussion closely, so my
apologies if I am off-topic. But on Ubuntu 18.04 at
least you can run

  sudo apt install openjdk-11-jdk
  R CMD javareconf -e

and then in R

  install.packages("rJava")

should work.

kind regards
        Enrico

    >> From: "Johannes Ranke" <johannes.ranke at jrwb.de>
    >> To: "r-sig-debian" <r-sig-debian at r-project.org>,
"Chris Evans"
    >> <chrishold at psyctc.org>
    >> Sent: Tuesday, 22 January, 2019 08:47:28
    >> Subject: Re: [R-sig-Debian] So nearly there, but can't install
rJava

    >> Am Dienstag, 22. Januar 2019, 08:27:14 CET schrieb Chris Evans:

    >> ...

    >> > error: jni.h: No such file or directory

    >> > #include <jni.h>

    >> > ^

    >> > compilation terminated.

    >> You get a complaint that jni.h is missing. So one strategy would be
to look for
    >> this file in the available packages:

    >> sudo apt-file search jni.h

    >> One of the packages returned is openjdk-8-jdk-headless (which I
happen to have
    >> installed). I think (others will know for certain) that you need a
Java
    >> Development Kit (jdk) not just a runtime environment (jre).

    >> Cheers,

    >> Johannes

    Chris> -- 
    Chris> Chris Evans <chris at psyctc.org> Skype: chris-psyctc 
    Chris> Visiting Professor, University of Sheffield <chris.evans at
sheffield.ac.uk>
    Chris> 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.
    Chris> 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/
    Chris> 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!


-- 
Enrico Schumann
Lucerne, Switzerland
http://enricoschumann.net

Chris Evans

2019-Jan-22 13:45 UTC

head link

[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!

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