[Bug 2026834] Re: FTBFS: core dump during doxygen run

Tue Jul 11 17:53:57 UTC 2023

** Description changed:

  https://launchpadlibrarian.net/676600060/buildlog_ubuntu-mantic-
  amd64.fenics-dolfinx_1%3A0.6.0-4_BUILDING.txt.gz

- This might also be a bug in doxygen. It didn't happen in the other
- arches build (which were done days earlier than amd64), and is also not
- happening in debian.
+ Generating XML output for file generation.cpp
+ Generating XML output for file generation.h
+ Generating XML output ferror: Failed to extract bounding box from generated diagram file /<<PKGBUILDDIR>>/cpp/doc/latex/d2/d97/classdolfinx_1_1io_1_1FidesWriter__inherit__graph.pdf
+  (warning treated as error, aborting now)
+ Segmentation fault (core dumped)
+ make[1]: *** [debian/rules:168: override_dh_auto_install-indep] Error 139
+ make[1]: Leaving directory '/<<PKGBUILDDIR>>'
+ make: *** [debian/rules:125: binary] Error 2
+ dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2
+ 
+ 
+ This might also be a bug in doxygen. It didn't happen in the other arches build (which were done days earlier than amd64), and is also not happening in debian.

  From what I could see so far, in Ubuntu doxygen ends up calling dot, and
  dot errors with some file and exits. This exit status catches doxygen by
  surprise, and an atexit() handler crashes:

  Thread 7 "doxygen" received signal SIGSEGV, Segmentation fault.
  [Switching to Thread 0x7fffe5dfa6c0 (LWP 30404)]
- 0x00007fffeaa3eb03 in __run_exit_handlers (status=1, listp=0x7fffeabf6840 <__exit_funcs>, run_list_atexit=run_list_atexit at entry=true, 
-     run_dtors=run_dtors at entry=true) at ./stdlib/exit.c:72
- Download failed: Invalid argument.  Continuing without source file ./stdlib/./stdlib/exit.c.                                                                   
+ 0x00007fffeaa3eb03 in __run_exit_handlers (status=1, listp=0x7fffeabf6840 <__exit_funcs>, run_list_atexit=run_list_atexit at entry=true,
+     run_dtors=run_dtors at entry=true) at ./stdlib/exit.c:72
+ Download failed: Invalid argument.  Continuing without source file ./stdlib/./stdlib/exit.c.
  72      ./stdlib/exit.c: No such file or directory.
  (gdb) bt
- #0  0x00007fffeaa3eb03 in __run_exit_handlers (status=1, listp=0x7fffeabf6840 <__exit_funcs>, run_list_atexit=run_list_atexit at entry=true, 
-     run_dtors=run_dtors at entry=true) at ./stdlib/exit.c:72
+ #0  0x00007fffeaa3eb03 in __run_exit_handlers (status=1, listp=0x7fffeabf6840 <__exit_funcs>, run_list_atexit=run_list_atexit at entry=true,
+     run_dtors=run_dtors at entry=true) at ./stdlib/exit.c:72
  #1  0x00007fffeaa3ed20 in __GI_exit (status=<optimized out>) at ./stdlib/exit.c:141
  #2  0x0000555555d5778b in handle_warn_as_error () at /usr/src/doxygen-1.9.4-4/src/message.cpp:133
  #3  0x0000555555d57b2f in err (fmt=fmt at entry=0x555556356e38 "Failed to extract bounding box from generated diagram file %s\n")
-     at /usr/src/doxygen-1.9.4-4/src/message.cpp:237
- #4  0x0000555555caebe4 in DotRunner::readBoundingBox (fileName=..., width=width at entry=0x7fffe5df9920, height=height at entry=0x7fffe5df9924, 
-     isEps=isEps at entry=false) at /usr/src/doxygen-1.9.4-4/src/dotrunner.cpp:135
+     at /usr/src/doxygen-1.9.4-4/src/message.cpp:237
+ #4  0x0000555555caebe4 in DotRunner::readBoundingBox (fileName=..., width=width at entry=0x7fffe5df9920, height=height at entry=0x7fffe5df9924,
+     isEps=isEps at entry=false) at /usr/src/doxygen-1.9.4-4/src/dotrunner.cpp:135
  #5  0x0000555555cafae9 in DotRunner::run (this=0x555556e57860) at /usr/src/doxygen-1.9.4-4/src/dotrunner.cpp:216
  #6  0x0000555555cb13d5 in DotWorkerThread::run (this=0x555556bfee70) at /usr/src/doxygen-1.9.4-4/src/dotrunner.cpp:304
  #7  0x00007fffeaee6383 in std::execute_native_thread_routine (__p=0x55555728c770) at ../../../../../src/libstdc++-v3/src/c++11/thread.cc:104
  #8  0x00007fffeaa8f18a in start_thread (arg=<optimized out>) at ./nptl/pthread_create.c:444
  #9  0x00007fffeab1dbd0 in clone3 () at ../sysdeps/unix/sysv/linux/x86_64/clone3.S:81

- 
- 
  Investigation continues.

** Bug watch added: Debian Bug tracker #1040864
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1040864

** Also affects: doxygen (Debian) via
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1040864
   Importance: Unknown
       Status: Unknown

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https://bugs.launchpad.net/bugs/2026834

Title:
  FTBFS: core dump during doxygen run

Status in doxygen package in Ubuntu:
  In Progress
Status in doxygen package in Debian:
  Unknown

Bug description:
  https://launchpadlibrarian.net/676600060/buildlog_ubuntu-mantic-
  amd64.fenics-dolfinx_1%3A0.6.0-4_BUILDING.txt.gz

  Generating XML output for file generation.cpp
  Generating XML output for file generation.h
  Generating XML output ferror: Failed to extract bounding box from generated diagram file /<<PKGBUILDDIR>>/cpp/doc/latex/d2/d97/classdolfinx_1_1io_1_1FidesWriter__inherit__graph.pdf
   (warning treated as error, aborting now)
  Segmentation fault (core dumped)
  make[1]: *** [debian/rules:168: override_dh_auto_install-indep] Error 139
  make[1]: Leaving directory '/<<PKGBUILDDIR>>'
  make: *** [debian/rules:125: binary] Error 2
  dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2

  This might also be a bug in doxygen. It didn't happen in the other arches build (which were done days earlier than amd64), and is also not happening in debian.

  From what I could see so far, in Ubuntu doxygen ends up calling dot,
  and dot errors with some file and exits. This exit status catches
  doxygen by surprise, and an atexit() handler crashes:

  Thread 7 "doxygen" received signal SIGSEGV, Segmentation fault.
  [Switching to Thread 0x7fffe5dfa6c0 (LWP 30404)]
  0x00007fffeaa3eb03 in __run_exit_handlers (status=1, listp=0x7fffeabf6840 <__exit_funcs>, run_list_atexit=run_list_atexit at entry=true,
      run_dtors=run_dtors at entry=true) at ./stdlib/exit.c:72
  Download failed: Invalid argument.  Continuing without source file ./stdlib/./stdlib/exit.c.
  72      ./stdlib/exit.c: No such file or directory.
  (gdb) bt
  #0  0x00007fffeaa3eb03 in __run_exit_handlers (status=1, listp=0x7fffeabf6840 <__exit_funcs>, run_list_atexit=run_list_atexit at entry=true,
      run_dtors=run_dtors at entry=true) at ./stdlib/exit.c:72
  #1  0x00007fffeaa3ed20 in __GI_exit (status=<optimized out>) at ./stdlib/exit.c:141
  #2  0x0000555555d5778b in handle_warn_as_error () at /usr/src/doxygen-1.9.4-4/src/message.cpp:133
  #3  0x0000555555d57b2f in err (fmt=fmt at entry=0x555556356e38 "Failed to extract bounding box from generated diagram file %s\n")
      at /usr/src/doxygen-1.9.4-4/src/message.cpp:237
  #4  0x0000555555caebe4 in DotRunner::readBoundingBox (fileName=..., width=width at entry=0x7fffe5df9920, height=height at entry=0x7fffe5df9924,
      isEps=isEps at entry=false) at /usr/src/doxygen-1.9.4-4/src/dotrunner.cpp:135
  #5  0x0000555555cafae9 in DotRunner::run (this=0x555556e57860) at /usr/src/doxygen-1.9.4-4/src/dotrunner.cpp:216
  #6  0x0000555555cb13d5 in DotWorkerThread::run (this=0x555556bfee70) at /usr/src/doxygen-1.9.4-4/src/dotrunner.cpp:304
  #7  0x00007fffeaee6383 in std::execute_native_thread_routine (__p=0x55555728c770) at ../../../../../src/libstdc++-v3/src/c++11/thread.cc:104
  #8  0x00007fffeaa8f18a in start_thread (arg=<optimized out>) at ./nptl/pthread_create.c:444
  #9  0x00007fffeab1dbd0 in clone3 () at ../sysdeps/unix/sysv/linux/x86_64/clone3.S:81

  Investigation continues.

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