Markus Jäntti
2007-Oct-12 02:33 UTC
[R-sig-Debian] problems with java under debian (including the R help page search engine)
Dear List: this is a problem that affects my use of R under Debian, but is a problem with using the Java virtual machine. I am turning to this list, since I am hoping someone might have more experience with trying to figure out why Java does not work under Debian than I do. I apologize in advance for trying to exploit list knowledge for a problem that is only tangential to the list. I am experiencing strange problems using Java on my Debian unstable. When I am logged in as my normal user, the Java virtual machine invariable crashes (I paste in below the bud report broduced by bug buddy). I have tried uninstalling and re-installing my java -- the sun-java6-*, see below for output from dpkg --list -- to no avail. I uninstalled it and used various other java:s (including the ecj-gjc and so on), with little success. However, I then noticed this did not affect other users on my system. If I create a new user and fire up the R help search page, it works as it should. This led me to search for java settings under my standard account that are causing the crash, but not amount of using "strace" before using crashing Java applications, such as comparing for my regular userid and a new one the output of strace -o tmp.log /usr/lib/jvm/java-6-sun-1.6.0.03/bin/ControlPanel produced any hint I could understand. (I also experimented with moving $HOME/.java out of the way. Did not help. Trying to use the /usr/lib/jvm/java-6-sun-1.6.0.03/bin/ControlPanel (which crashes under my regular userid but not under alternative ones) and see what files under $HOME changed also did not give a hint. I have also tried to see if update-alternatives is wrong, but as the Java Virtual Machine works for other users, I can't really see how that would be the problem. hefaistos:/etc/alternatives# ls -l /etc/alternatives/iceweasel-javaplugin.so lrwxrwxrwx 1 root root 64 2007-10-11 21:55 /etc/alternatives/iceweasel-javaplugin.so -> /usr/lib/jvm/java-6-sun/jre/plugin/i386/ns7/libjavaplugin_oji.so Also, about:plugins in iceweasel shows the above plugin. Finally, I do not seem to have any java-related environment variables set in my $HOME/.bash_profile, $OME/.bashrc or $HOME/.profile, not do I have a Java Virtual Machine lurking under my $HOME. The simple solution might be to just start using a new username but this might just postpone the problem, rather than solve it. I would be very greatful for any suggestsions on how to find out what settings can cause such crashes. I add below the information on the Java packages and the bud-buddy bug report. TIA, Markus markus at hefaistos:~$ dpkg --list | grep sun-java6 ii sun-java6-bin 6-03-2 Sun Java(TM) Runtime Environment (JRE) 6 (ar ii sun-java6-demo 6-03-2 Sun Java(TM) Development Kit (JDK) 6 demos a ii sun-java6-doc 6-03-2 Sun JDK(TM) Documention -- integration insta ii sun-java6-fonts 6-03-2 Lucida TrueType fonts (from the Sun JRE) ii sun-java6-jdk 6-03-2 Sun Java(TM) Development Kit (JDK) 6 ii sun-java6-jre 6-03-2 Sun Java(TM) Runtime Environment (JRE) 6 (ar ii sun-java6-plugin 6-03-2 The Java(TM) Plug-in, Java SE 6 markus at hefaistos:~/Desktop$ cat "<unknown>-bugreport.txt" --System: Linux 2.6.22-2-686 #1 SMP Fri Aug 31 00:24:01 UTC 2007 i686 X Vendor: The X.Org Foundation X Vendor Release: 70000000 Selinux: No Accessibility: Disabled GTK+ Theme: Industrial Icon Theme: gnome Memory status: size: 234995712 vsize: 234995712 resident: 23953408 share: 13811712 rss: 23953408 rss_rlim: 4294967295 CPU usage: start_time: 1192126999 rtime: 23 utime: 21 stime: 2 cutime:0 cstime: 0 timeout: 0 it_real_value: 0 frequency: 100 Backtrace was generated from '/usr/lib/bug-buddy/<unknown>' Using host libthread_db library "/lib/i686/cmov/libthread_db.so.1". [Thread debugging using libthread_db enabled] [New Thread 0xb7dd66b0 (LWP 22831)] [New Thread 0xb4d97b90 (LWP 22844)] [New Thread 0xb4de8b90 (LWP 22842)] [New Thread 0xb4e39b90 (LWP 22841)] [New Thread 0xb506bb90 (LWP 22840)] [New Thread 0xb50ffb90 (LWP 22839)] [New Thread 0xb562cb90 (LWP 22838)] [New Thread 0xb567db90 (LWP 22837)] [New Thread 0xb56feb90 (LWP 22836)] [New Thread 0xb574fb90 (LWP 22835)] [New Thread 0xb5b4cb90 (LWP 22834)] [New Thread 0xb5b9db90 (LWP 22833)] [New Thread 0xb5c1eb90 (LWP 22832)] 0xffffe410 in __kernel_vsyscall () #0 0xffffe410 in __kernel_vsyscall () #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 #3 0x0630b2d9 in os::PlatformEvent::park () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so #4 0x06362e95 in ObjectMonitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so #5 0x063606ff in ObjectSynchronizer::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so #6 0x0625defa in JVM_MonitorWait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so #7 0xb5d3a68e in ?? () #8 0x080524ec in ?? () #9 0xbfc195e0 in ?? () #10 0x00000000 in ?? () Thread 13 (Thread 0xb5c1eb90 (LWP 22832)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d8fc in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd9f in pthread_cond_timedwait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x062f978e in Monitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x063c4ab7 in VMThread::loop () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x063c446f in VMThread::run () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0630b719 in java_start () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb7f2946b in start_thread () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #8 0xb7eaa6de in clone () from /lib/i686/cmov/libc.so.6 No symbol table info available. Thread 12 (Thread 0xb5b9db90 (LWP 22833)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x0630b2d9 in os::PlatformEvent::park () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x06362e95 in ObjectMonitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x063606ff in ObjectSynchronizer::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0625defa in JVM_MonitorWait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb5d3a68e in ?? () No symbol table info available. #8 0x0807a8ec in ?? () No symbol table info available. #9 0xb5b9cd50 in ?? () No symbol table info available. #10 0x00000000 in ?? () No symbol table info available. Thread 11 (Thread 0xb5b4cb90 (LWP 22834)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x0630b2d9 in os::PlatformEvent::park () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x06362e95 in ObjectMonitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x063606ff in ObjectSynchronizer::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0625defa in JVM_MonitorWait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb5d3a68e in ?? () No symbol table info available. #8 0x0807b8ec in ?? () No symbol table info available. #9 0xb5b4bd9c in ?? () No symbol table info available. #10 0x00000000 in ?? () No symbol table info available. Thread 10 (Thread 0xb574fb90 (LWP 22835)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2f65e in sem_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0x0630ba64 in check_pending_signals () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #3 0x0630900d in os::signal_wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x06306218 in signal_thread_entry () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x06384190 in JavaThread::run () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0630b719 in java_start () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb7f2946b in start_thread () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #8 0xb7eaa6de in clone () from /lib/i686/cmov/libc.so.6 No symbol table info available. Thread 9 (Thread 0xb56feb90 (LWP 22836)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x062f9871 in Monitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x0618fdae in CompileQueue::get () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x061916c5 in CompileBroker::compiler_thread_loop () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x06384190 in JavaThread::run () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0x0630b719 in java_start () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #8 0xb7f2946b in start_thread () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #9 0xb7eaa6de in clone () from /lib/i686/cmov/libc.so.6 No symbol table info available. Thread 8 (Thread 0xb567db90 (LWP 22837)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x062f96e6 in Monitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x062dcf84 in LowMemoryDetector::low_memory_detector_thread_entry () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x06384190 in JavaThread::run () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0630b719 in java_start () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb7f2946b in start_thread () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #8 0xb7eaa6de in clone () from /lib/i686/cmov/libc.so.6 No symbol table info available. Thread 7 (Thread 0xb562cb90 (LWP 22838)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d8fc in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd9f in pthread_cond_timedwait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x06309aab in os::sleep () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x0638349a in WatcherThread::run () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x0630b719 in java_start () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0xb7f2946b in start_thread () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #7 0xb7eaa6de in clone () from /lib/i686/cmov/libc.so.6 No symbol table info available. Thread 6 (Thread 0xb50ffb90 (LWP 22839)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x0630b2d9 in os::PlatformEvent::park () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x06362e95 in ObjectMonitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x063606ff in ObjectSynchronizer::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0625defa in JVM_MonitorWait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb5d3a68e in ?? () No symbol table info available. #8 0xb511b8ec in ?? () No symbol table info available. #9 0xb50fefec in ?? () No symbol table info available. #10 0x00000000 in ?? () No symbol table info available. Thread 5 (Thread 0xb506bb90 (LWP 22840)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7ea05e7 in poll () from /lib/i686/cmov/libc.so.6 No symbol table info available. #2 0xb540654e in performPoll () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/xawt/libmawt.so No symbol table info available. #3 0xb5406363 in waitForEvents () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/xawt/libmawt.so No symbol table info available. #4 0xb5d3a68e in ?? () No symbol table info available. #5 0xb51518ec in ?? () No symbol table info available. #6 0xffffffff in ?? () No symbol table info available. #7 0xffffffff in ?? () No symbol table info available. #8 0xffffffff in ?? () No symbol table info available. #9 0xb506ac6c in ?? () No symbol table info available. #10 0xb506ac8c in ?? () No symbol table info available. #11 0xb5d32edd in ?? () No symbol table info available. #12 0xb506ac6c in ?? () No symbol table info available. #13 0x00000000 in ?? () No symbol table info available. Thread 4 (Thread 0xb4e39b90 (LWP 22841)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x0630b2d9 in os::PlatformEvent::park () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x06362e95 in ObjectMonitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x063606ff in ObjectSynchronizer::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0625defa in JVM_MonitorWait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb5d3a68e in ?? () No symbol table info available. #8 0xb515b8ec in ?? () No symbol table info available. #9 0xb4e38d4c in ?? () No symbol table info available. #10 0x00000000 in ?? () No symbol table info available. Thread 3 (Thread 0xb4de8b90 (LWP 22842)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d8fc in pthread_cond_timedwait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd9f in pthread_cond_timedwait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x0630c0e1 in os::Linux::Event::timedwait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x063099a5 in os::sleep () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x0626e5d0 in JVM_Sleep () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0xb5d3a68e in ?? () No symbol table info available. #7 0xb5160cec in ?? () No symbol table info available. #8 0xb4de7dcc in ?? () No symbol table info available. #9 0x000007d0 in ?? () No symbol table info available. #10 0x00000000 in ?? () No symbol table info available. Thread 2 (Thread 0xb4d97b90 (LWP 22844)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f3114b in waitpid () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb486a624 in g_spawn_sync () from /usr/lib/libglib-2.0.so.0 No symbol table info available. #3 0xb486a93c in g_spawn_command_line_sync () from /usr/lib/libglib-2.0.so.0 No symbol table info available. #4 0xb5019238 in ?? () from /usr/lib/gtk-2.0/modules/libgnomebreakpad.so No symbol table info available. #5 <signal handler called> No symbol table info available. #6 0xb5d40ab8 in ?? () No symbol table info available. #7 0xb5d32d77 in ?? () No symbol table info available. #8 0x00000000 in ?? () No symbol table info available. Thread 1 (Thread 0xb7dd66b0 (LWP 22831)): #0 0xffffe410 in __kernel_vsyscall () No symbol table info available. #1 0xb7f2d676 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #2 0xb7f2dd28 in pthread_cond_wait at GLIBC_2.0 () from /lib/i686/cmov/libpthread.so.0 No symbol table info available. #3 0x0630b2d9 in os::PlatformEvent::park () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #4 0x06362e95 in ObjectMonitor::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #5 0x063606ff in ObjectSynchronizer::wait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #6 0x0625defa in JVM_MonitorWait () from /usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/i386/client/libjvm.so No symbol table info available. #7 0xb5d3a68e in ?? () No symbol table info available. #8 0x080524ec in ?? () No symbol table info available. #9 0xbfc195e0 in ?? () No symbol table info available. #10 0x00000000 in ?? () No symbol table info available. #0 0xffffe410 in __kernel_vsyscall () The program is running. Quit anyway (and detach it)? (y or n) [answered Y; input not from terminal] ----------- .xsession-errors --------------------- /usr/lib/bug-buddy/<unknown>: No such file or directory. Could not read ack from child process Plugin: Java VM process has died. plugin: java process exited with status 0 Could not start JavaVM! VM did not start up properly /usr/lib/bug-buddy/<unknown>: No such file or directory. Could not read ack from child process Plugin: Java VM process has died. plugin: java process exited with status 0 Could not start JavaVM! VM did not start up properly /usr/lib/bug-buddy/<unknown>: No such file or directory. -------------------------------------------------- Markus Jantti Abo Akademi University markus.jantti at iki.fi http://www.iki.fi/~mjantti