On Wed, 9 Sep 2020 at 10:57, Ranjan Maitra <mai...@email.com> wrote: > On Wed, 9 Sep 2020 08:08:23 -0300 "George N. White III" <gnw...@gmail.com> > wrote: > > > On Tue, 8 Sep 2020 at 18:34, Ranjan Maitra <mai...@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
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