Thanks, there has been no activity on the BZ report yet. Hopefully, this can be fixed soon, and I understand it is possible that it may be a memory leak in one of the R components. For instance, this morning, I noticed that even running the histogram command twice crashes the JGR window. I wonder if the issue also happens with Fedora 31.
Ranjan
On Thu, 10 Sep 2020 07:19:27 -0300 "George N. White III" gnwiii@gmail.com wrote:
On Wed, 9 Sep 2020 at 16:33, Jerry James loganjerry@gmail.com wrote:
On Wed, Sep 9, 2020 at 1:12 PM Ranjan Maitra maitra@email.com wrote:
Thanks, so this appears to be a Fedora problem. Btw, I tried oracle's
jdk-14.0.2_linux-x64_bin.rpm and had the same result.
I filed a bug report:
https://bugzilla.redhat.com/show_bug.cgi?id=1877524
Why does everyone seem to think this is a Java bug?
My system generated crash report (including a core dump) that identified a segfault in the Java runtime. A Java process is started by JGR(). JavaGD() seems to start another Java process
The OP's log starts with segfaults (signal 11) in a Java process: 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 Sep 9 08:51:12 localhost kernel: audit: type=1701 audit(1599659472.313:4973): 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
The system log
showed that a crash occurred in Rf_eval (libR.so + 0x157ab3); i.e., in the R library. The stack trace shows a lot of calls to these functions:
bcEval forcePromise getvar R_execClosure Rf_appyClosure Rf_eval
It's possible that R is being handed an expression to evaluate that is so complex that it runs out of stack space, or there could be an infinite recursion bug in R somewhere. If the former, the solution is to bump up the stack space. I would try the -Xss argument to java first to see if that makes the issue go away. I'm not sure what the default value is, so I don't know what to suggest, but maybe start with something like -Xss4M. If that fixes the issue, then retry with successively smaller values to find something reasonable that is still big enough to work.
The problem seems to be specific to Fedora 32.
-- Jerry James http://www.jamezone.org/ _______________________________________________ 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
-- George N. White III
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