R SIG Debian - Jun 2017 - rJava Broken on Linux + R 3.4

Hi Dirk,
It was unclear to me to which extent it is a
kernel/security patch vs (r)Java issue.

In any case, this is really problematic for me as it prevents me de
facto from running some key R packages for my daily work.
I'll post again if I see some solution (other than downgrading the
kernel) somewhere.
Meanwhile, any suggestions for a fix is welcome.
Cheers

Lorenzo


On Mon, Jun 26, 2017 at 06:19:11AM -0500, Dirk Eddelbuettel
wrote:
>
>On 26 June 2017 at 10:43, Lorenzo Isella wrote:
>| Dear All,
>| I think there is something wrong with rJava on any Debian based
>| distribution.
>
>It is a Java issue related to a security fix many (most? all?) distros
>applied.
>
>| I may be wrong, but I experiencing exactly the problems mentioned at
>|
>| https://github.com/amattioc/SDMX/issues/130
>|
>| and at
>|
>| https://github.com/s-u/rJava/issues/110
>|
>| A couple of packages (RJSDMX and xlsx) are now impossible to install
>| on my debian stretch platform running R 3.4.
>|
>| It seems I am not the only one experiencing this and it may be due to
>| some security patches just released.
>| However, if I run on my machine
>|
>| > library(rJava)
>| > .jinit()
>|
>| I get a segmentation fault, though I was able to install rJava, it
>| does not seem to work properly.
>| Does anyone have a fix for that?
>
>Reading the links you providing it also becomes clear that this is not an
>issue with rJava, or Debian -- it is Java, interacting with the kernel.
>
>For now, I would suggest following those discussions.
>
>Dirk
>
>-- 
>http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

For those going to UseR! in Brussels, maybe a short meeting over coffee
to make some notes about the issues. I know I've had troubles before with
rJava over the years, and I won't pretend to be much more than a recipe
follower. However, if it's possible to have a few notes on "where to
look" for diagnostics and fixes, or even explaining what is going wrong,
I'll be happy to write them up and post somewhere. I've been doing such
short how-to items on our oclug.on.ca wiki for other software, and feedback
has been positive.

Best, JN

On 2017-06-26 08:40 AM, Lorenzo Isella wrote:
> Hi Dirk,
> It was unclear to me to which extent it is a
> kernel/security patch vs (r)Java issue.
> 
> In any case, this is really problematic for me as it prevents me de
> facto from running some key R packages for my daily work.
> I'll post again if I see some solution (other than downgrading the
> kernel) somewhere.
> Meanwhile, any suggestions for a fix is welcome.
> Cheers
> 
> Lorenzo
> 
> 
> On Mon, Jun 26, 2017 at 06:19:11AM -0500, Dirk Eddelbuettel wrote:
>>
>> On 26 June 2017 at 10:43, Lorenzo Isella wrote:
>> | Dear All,
>> | I think there is something wrong with rJava on any Debian based
>> | distribution.
>>
>> It is a Java issue related to a security fix many (most? all?) distros
>> applied.
>>
>> | I may be wrong, but I experiencing exactly the problems mentioned at
>> |
>> | https://github.com/amattioc/SDMX/issues/130
>> |
>> | and at
>> |
>> | https://github.com/s-u/rJava/issues/110
>> |
>> | A couple of packages (RJSDMX and xlsx) are now impossible to install
>> | on my debian stretch platform running R 3.4.
>> |
>> | It seems I am not the only one experiencing this and it may be due to
>> | some security patches just released.
>> | However, if I run on my machine
>> |
>> | > library(rJava)
>> | > .jinit()
>> |
>> | I get a segmentation fault, though I was able to install rJava, it
>> | does not seem to work properly.
>> | Does anyone have a fix for that?
>>
>> Reading the links you providing it also becomes clear that this is not
an
>> issue with rJava, or Debian -- it is Java, interacting with the kernel.
>>
>> For now, I would suggest following those discussions.
>>
>> Dirk
>>
>> -- 
>> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

On 27 June 2017 at 12:56, Simon Urbanek wrote:
| I have seen a report on GH but I'm traveling abroad so can't easily
reproduce. It's really odd as the issue reportedly only appears after Debian
kernel upgrade - especially that it's an old kernel with a Debian patch that
breaks it. The big question is if it's related to our JNI code or in JVM
itself or a bug in the kernel patch.

FWIW I first heard about it at work last week when a CVE suggested security
patch (for CentOS) broke a commercial Java-based scheduling app _hard_ to the
extent that their engineers threw their hands up and suggested to wait for a
fix by Oracle (yeah, right) for Java.

As I understand it, a system-level fix affecting the Java layer. Not rJava.

Dirk

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