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@xxxxxxxxx> wrote: > On Wed, 9 Sep 2020 at 10:57, Ranjan Maitra <maitra@xxxxxxxxx> wrote: > > > On Wed, 9 Sep 2020 08:08:23 -0300 "George N. White III" <gnwiii@xxxxxxxxx> > > wrote: > > > > > On Tue, 8 Sep 2020 at 18:34, Ranjan Maitra <maitra@xxxxxxxxx> 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. 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