Thanks, I will file the bug report: should it be upstream or on Fedora? I know about Fedora's BZ, but what is upstream?

Ranjan

On Wed, 9 Sep 2020 13:15:57 -0300 "George N. White III" <gnwiii@gmail.com> wrote:

> On Wed, 9 Sep 2020 at 10:57, Ranjan Maitra <maitra@email.com> wrote:
>
> > On Wed, 9 Sep 2020 08:08:23 -0300 "George N. White III" <gnwiii@gmail.com>
> > wrote:
> >
> > > On Tue, 8 Sep 2020 at 18:34, Ranjan Maitra <maitra@email.com> wrote:
> > >
> > > > Dear friends,
> > > >
> > > > I have a strange situation that shows up only on F32 (only linux
> > > > distributions tried) but does not show up on Windoze or Muck. The way
> > to
> > > > illustrate this is rather complicated, so I will first summarize.
> > > >
> > > > For my introductory students, I use a java-based front-end to R called
> > > > Deducer. I am able to install without a hitch and even bring it up and
> > run
> > > > some functions and graphical displays. However, when I ask it to do a
> > few
> > > > specific functions, the windows all come crashing down. So, my
> > question is:
> > > > how do I figure out the source of the problem? I have used this
> > program for
> > > > years, and including last spring under F31, and linux has never been an
> > > > issue. This has been tried on three F32 machines by me and a former
> > student
> > > > and all have resulted in crashes. Embarrasingly, these continue to
> > work as
> > > > expected with Windows and MacOS, though installation, especially for
> > the
> > > > latter is a pain.
> > > >
> > >
> > > It would be good to mention enough detail so others can reproduce your
> > > configuration:
> > >
> > > graphics hardware and driver: did the 3 machines use the same graphics
> > > hardware and drivers?
> >
> > Hi,
> >
> > Thanks! The 3 machines are very different (all laptops, though) so likely
> > have different graphics HW and drivers.
> >
> > > graphics display server: wayland +xwayland or X11
> >
> > Sorry, how do I figure this out? I think one of the machines uses gnome so
> > whatever comes with that (likely wayland +xwayland?) and mine I think uses
> > X11 (these use openbox).
> >
> >
> I tried both wayland and weston in Fedroa 32 as a VM.   It is the JRE that
> crashes.  My system generated a problem report (which fails to upload -- I
> think the server is down) for java-1.8.0-openjdk-headless, which is odd
> considering the application uses graphics.
>
>
> > > JRE -- some Java apps require Oracle's proprietary JRE
> >
> > I am using the default Fedora version, and also tried with fedora's
> > java-latest. Importantly, upto F31, this has never been an issue.
> >
> > >
> > > > How can I get error messages out of this mishap to file a meaningful
> > and
> > > > targeted bug report?
> > > >
> > >
> > >  https://www.linuxjournal.com/content/oops-debugging-kernel-panics-0
> > >
> > >
> > > >
> > > > Any suggestions?
> > > > Ranjan
> > > >
> > > >
> > > > If you are interested, here is how I go about installing Deducer. I
> > need
> > > > R-core installed, as well as curl-devel, and of course java. Other
> > fedora
> > > > packages may also be needed.
> > > >
> > > > sudo dnf install R-devel curl-devel java-1.8.0-openjdk-devel
> > > >
> > > > then:
> > > >
> > > > sudo R
> > > > install.packages(c('JGR','Deducer'))
> > > > q()
> > > >
> > > > Note that the second line will ask for which repo to use, and any are
> > > > fine, the first one is from rstudio.com. Also, the installation
> > function
> > > > may ask for more libraries to be installed.
> > > >
> > > > Once installed, go to R and inside R, type:
> > > >
> > > > library(JGR)
> > > > library(Deducer)
> > > > JGR()
> > > >
> > > > The last function call will open a graphical interface with a jaguar
> > logo
> > > > (pretty cool). All is well. In the bottom window type:
> > > > data(cars)
> > > >
> > > > Then go to the graphical interface above, and under "Plots" -> "Quick"
> > ->
> > > > "simple boxplot"
> > > > This opens a window, and put speed as x variable and run.
> > > > A window begins to open and the entire window system running JGR comes
> > > > crashing down.
> > >
> > >
> > > > Btw, since I know the commands to give in R, on the commandline, when I
> > > > call the function, things work as expected. It is only on the JGR()
> > window
> > > > that it crashes.
> > > >
> > >
> > > Have you checked rJava and JGR bug reports?
> >
> > I looked around but was unable to find this specific crash detailed
> > anywhere.
> >
> >
> > > >
> > > > The worst part? I get no error messages. So, how can I get error
> > messages
> > > > out of this mishap to file a meaningful and targeted bug report?
> > > >
> > > > Can you connect to the system with ssh or use a console <Alt Fn>? If so
> > > the kernel is still alive and the graphics system has crashed.  If not,
> > > you can first try adjusting your configuration.  The last resort is
> > kernel
> > > debugging.
> >
> > Yes, the system and the graphics itself is up and running. It is only the
> > JGR window that crashes (and brings down that part of the program). What
> > surprises me is that only certain parts of the program crash. For instance,
> > the histograph and density plots or scatterplot (both also using ggplot2
> > software) get displayed fine.
> >
> >
> >
> > So, your message set me thinking of looking at
> >
> > tail -f /var/log/messages
> >
> > while there is a successful operation, such as using the histogram
> > function, and an operation (boxplot) which crashes. Here is the output for
> > when it succeeds (displays a histogram):
> >
> >
> > [...]
> >
> >
> >
> > Here is the output for when it crashes (displays a boxplot):
> >
> >
> > Sep  9 08:51:12 localhost audit[53948]: ANOM_ABEND auid=1000 uid=1000
> > gid=1000 ses=2 subj=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023
> > pid=53948 comm="Thread-5"
> > exe="/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.265.b01-1.fc32.x86_64/jre/bin/java"
> > sig=11 res=1
> > >
> > > This suggests a graphics issue. If you have been using wayland you should
> > > try the X11 server.   if both graphics systems are failing you could try
> > an
> > > Oracle JRE
> > >
> > https://www.oracle.com/java/technologies/javase/javase8-archive-downloads.html
> >
> > I could do that, I guess, but does the above help?
> >
>
> I can reproduce the problem.  It merits a bug report against openJDK (best
> if you report it as
> I may be otherwise busy and not able to keep up with requests for more info
> or  testing
> potential fixes).
>
> --
> George N. White III


--
Important Notice: This mailbox is ignored: e-mails are set to be deleted on receipt. Please respond to the mailing list if appropriate. For those needing to send personal or professional e-mail, please use appropriate addresses.
_______________________________________________
users mailing list -- users@lists.fedoraproject.org
To unsubscribe send an email to users-leave@lists.fedoraproject.org
Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/
List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines
List Archives: https://lists.fedoraproject.org/archives/list/users@lists.fedoraproject.org