bugGnome Chemistry Utils - Bugs: bug #39793, MacPorts build log


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bug #39793: MacPorts build log

Submitted by:  C. Herbig <mapatxe42>
Submitted on:  Fri 16 Aug 2013 04:09:49 AM UTC  
Category:  None Severity:  3 - Normal
Item Group:  None Status:  None
Privacy:  Public Assigned to:  None
Open/Closed:  Open

( Jump to the original submission)

Tue 27 Aug 2013 11:00:08 PM UTC, comment #14: 

Unfortunately I cannot spend any more time on this right now.  As far as I can tell, gchempaint (the one that I care the most about) and gcrystal both work as expected, I don't have any files to test gchem3D or gspectrum though, but nobody has yet complained that they don't work.  I'll dabble with trying to get an IDE debugger working with it, but I guess for now gchemtable and gchemcalc will simply remain broken on OS X.  If anything new comes up I will certainly let you know, meanwhile, thank you for trying to help.

C. Herbig <mapatxe42>
Fri 23 Aug 2013 06:17:02 AM UTC, comment #13: 

I'm using Anjuta for development, but not for debugging. I generally use gdb from the command line, along with some printf debug.

Jean Bréfort <jean_brefort>
Project Administrator
Thu 22 Aug 2013 08:37:14 PM UTC, comment #12: 

Do you use an IDE for development and debugging?  I was trying to configure Xcode to work with it, but not much luck.

C. Herbig <mapatxe42>
Thu 22 Aug 2013 05:59:23 AM UTC, comment #11: 

Quite weird. I'm unable to debug this without an appropriate machine at hand. As the crash seems to occur in the std::locale constructor, you might try to remove the corresponding lines in libs/gcu/chemistry.cc and test again.

Jean Bréfort <jean_brefort>
Project Administrator
Wed 21 Aug 2013 07:37:23 PM UTC, comment #10: 

Nope, still crashes with the same messages.

C. Herbig <mapatxe42>
Wed 21 Aug 2013 07:14:00 AM UTC, comment #9: 

Attached patch might solve at least the gchemtable issue. Please test.
The stack trace from gchemcal does not provide enough information (no reference to any gchemutils code).

(file #28895)

Jean Bréfort <jean_brefort>
Project Administrator
Mon 19 Aug 2013 08:24:08 PM UTC, comment #8: 

For now we have blacklisted the clang compiler in favor of llvm-gcc.  Also, compiling against some updated gnome libraries seems to fix the gchempaint close button problem, regardless of clang vs gcc, these updated libraries are not yet committed in the public MacPorts tree yet.  The only things that seem to be problematic right now are gchemtable crashes on launch, and gchemcalc launches, but crashes once a formula is entered.

I will go ahead and cross-reference the discussion on the MacPorts bug tracker here: https://trac.macports.org/ticket/40145#

C. Herbig <mapatxe42>
Mon 19 Aug 2013 08:19:27 PM UTC, comment #7: 

Stil trying to get all of the dependencies compiled with -g or --enable-debug so that the backtrack shows more than just "No symbol table info available." for everything.

Meanwhile, here is a crash log for gchemtable:

  1.   libsystem_kernel.dylib        0x00007fff9139e212 __pthread_kill + 10

1   libsystem_c.dylib             0x00007fff98533b54 pthread_kill + 90
2   libsystem_c.dylib             0x00007fff98577dce abort + 143
3   libc++abi.dylib               0x00007fff935bb9eb abort_message + 257
4   libc++abi.dylib               0x00007fff935b939a default_terminate() + 28
5   libobjc.A.dylib               0x00007fff9689d887 _objc_terminate() + 111
6   libc++abi.dylib               0x00007fff935b93c9 safe_handler_caller(void (*)()) + 8
7   libc++abi.dylib               0x00007fff935b9424 std::terminate() + 16
8   libc++abi.dylib               0x00007fff935ba58b __cxa_throw + 111
9   libstdc++.6.dylib             0x00007fff94dd14b8 std::__throw_runtime_error(char const*) + 85
10  libstdc++.6.dylib             0x00007fff94e0c237 std::locale::facet::_S_create_c_locale(int*&, char const*, int*) + 47
11  libstdc++.6.dylib             0x00007fff94dd4af1 std::locale::_Impl::_Impl(char const*, unsigned long) + 77
12  libstdc++.6.dylib             0x00007fff94dd42cd std::locale::locale(char const*) + 135
13  libgcu-0.14.0.dylib           0x0000000105617274 gcu_value_get_string + 61
14  libgcu-0.14.0.dylib           0x0000000105617481 gcu_element_get_weight_as_string + 83
15  libgcugtk-0.14.0.dylib        0x00000001055c3f56 gcu_periodic_set_tips + 329
16  gchemtable                    0x000000010558fad7 GChemTableApp::GChemTableApp() + 1077
17  gchemtable                    0x000000010558e396 main + 82
18  libdyld.dylib                 0x00007fff972127e1 start + 1

And for gchemcalc:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread

  1.   libsystem_kernel.dylib        0x00007fff9139e212 __pthread_kill + 10

1   libsystem_c.dylib             0x00007fff98533b54 pthread_kill + 90
2   libsystem_c.dylib             0x00007fff98577dce abort + 143
3   libsystem_c.dylib             0x00007fff9854b9b9 free + 392
4   ???                           0x00007f815a4a0b20 0 + 140193542310688
5   libgobject-2.0.0.dylib        0x00000001089ac8b0 g_closure_invoke + 281
6   libgobject-2.0.0.dylib        0x00000001089bf8af signal_emit_unlocked_R + 2025
7   libgobject-2.0.0.dylib        0x00000001089bf02c g_signal_emitv + 548
8   libgtk-3.0.dylib              0x0000000107ff6d7b gtk_binding_entry_activate + 1472
9   libgtk-3.0.dylib              0x0000000107ff82a5 binding_activate + 88
10  libgtk-3.0.dylib              0x0000000107ff8159 gtk_bindings_activate_list + 273
11  libgtk-3.0.dylib              0x0000000107ff822c gtk_bindings_activate_event + 153
12  libgtk-3.0.dylib              0x0000000108061d4b gtk_entry_key_press + 246
13  libgtk-3.0.dylib              0x00000001080be6c5 _gtk_marshal_BOOLEAN__BOXEDv + 198
14  libgobject-2.0.0.dylib        0x00000001089aca83 _g_closure_invoke_va + 202
15  libgobject-2.0.0.dylib        0x00000001089c0195 g_signal_emit_valist + 1225
16  libgobject-2.0.0.dylib        0x00000001089c0ba2 g_signal_emit + 134
17  libgtk-3.0.dylib              0x00000001081c7782 gtk_widget_event_internal + 452
18  libgtk-3.0.dylib              0x00000001081d99a7 gtk_window_propagate_key_event + 154
19  libgtk-3.0.dylib              0x00000001081ddb7d gtk_window_key_press_event + 33
20  libgtk-3.0.dylib              0x00000001080be5a7 _gtk_marshal_BOOLEAN__BOXED + 115
21  libgobject-2.0.0.dylib        0x00000001089ac8b0 g_closure_invoke + 281
22  libgobject-2.0.0.dylib        0x00000001089bfa1a signal_emit_unlocked_R + 2388
23  libgobject-2.0.0.dylib        0x00000001089c0525 g_signal_emit_valist + 2137
24  libgobject-2.0.0.dylib        0x00000001089c0ba2 g_signal_emit + 134
25  libgtk-3.0.dylib              0x00000001081c7782 gtk_widget_event_internal + 452
26  libgtk-3.0.dylib              0x00000001080bdfb1 propagate_event + 228
27  libgtk-3.0.dylib              0x00000001080bd717 gtk_main_do_event + 1441
28  libgdk-3.0.dylib              0x00000001084eae96 gdk_event_source_dispatch + 39
29  libglib-2.0.0.dylib           0x0000000108a267c2 g_main_context_dispatch + 276
30  libglib-2.0.0.dylib           0x0000000108a26ae2 g_main_context_iterate + 418
31  libglib-2.0.0.dylib           0x0000000108a26d36 g_main_loop_run + 207
32  libgtk-3.0.dylib              0x00000001080bd03f gtk_main + 74
33  gchemcalc                     0x0000000107c21ba7 main + 2422
34  libdyld.dylib                 0x00007fff972127e1 start + 1

C. Herbig <mapatxe42>
Sun 18 Aug 2013 06:14:06 AM UTC, comment #6: 

You need to ask gdb a backtrace with the 'bt' instruction or 'bt full' just after the crash.

Jean Bréfort <jean_brefort>
Project Administrator
Sun 18 Aug 2013 05:24:53 AM UTC, comment #5: 

The reason I was trying to get it working with Anjuta is that gdb from the command line is only saying the same thing as comment 2, and setting the breakpoints isn't working the way I expected it to.  So, I'm still trying to work on that...

C. Herbig <mapatxe42>
Fri 16 Aug 2013 07:30:47 AM UTC, comment #4: 

I've been trying to get that to work by installing Anjuta, but that has not been cooperative.  Meanwhile, gcc isn't bothered by the virtual overloads like clang is (perhaps that is actually a problem with clang...), and mainly only complains about deprecated methods, but the runtime errors persist.  I'll attach the build log from the llvm-gcc42 compiler, as it might be clearer.

(file #28861)

C. Herbig <mapatxe42>
Fri 16 Aug 2013 07:21:12 AM UTC, comment #3: 

Can you try to run the program inside a debugger and show a stack trace of the crash?

Jean Bréfort <jean_brefort>
Project Administrator
Fri 16 Aug 2013 07:15:48 AM UTC, comment #2: 

I have no idea what those warnings even mean.
The main runtime error that the apps throw is this:
   libc++abi.dylib: terminate called throwing an exception
   Abort trap: 6
Not very helpful...

C. Herbig <mapatxe42>
Fri 16 Aug 2013 07:01:00 AM UTC, comment #1: 

The most seen warning is:

:info:build ../libs/gcu/document.h:139:15: warning: 'gcu::Document::Save' hides overloaded virtual function [-Woverloaded-virtual]
:info:build         virtual void Save () const {;}
:info:build                      ^
:info:build ../libs/gcu/object.h:288:21: note: hidden overloaded virtual function 'gcu::Object::Save' declared here
:info:build         virtual xmlNodePtr Save (xmlDocPtr xml) const;

As the two virtual methods have different signatures, I don't see first why one of them can hide the other, and last how it would be harmful.

Jean Bréfort <jean_brefort>
Project Administrator
Fri 16 Aug 2013 04:09:49 AM UTC, original submission:  

Here is the build log containing many warnings for attempting to build gnome-chemistry-utils via macports.  Perhaps fixing some of these errors will fix some of the odd behavior of the suite on the mac-x11 platform.  This was generated using the default llvm-clang compiler.  If you want I can also prepare a build log using the llvm-gcc4.2 compiler.

C. Herbig <mapatxe42>


Attached Files
file #28895:  39793.patch added by jean_brefort (888B - text/x-patch - Patch to test.)
file #28861:  gnome-chemistry-utils_build-gcc.log added by mapatxe42 (77KiB - application/octet-stream - used llvm-gcc4.2 instead of llvm-clang)
file #28860:  gnome-chemistry-utils_build.log added by mapatxe42 (240KiB - application/octet-stream)


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    Follow 3 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2013-08-21 jean_brefort Attached File- => Added 39793.patch, #28895
    2013-08-16 mapatxe42 Attached File- => Added gnome-chemistry-utils_build-gcc.log, #28861
    2013-08-16 mapatxe42 Attached File- => Added gnome-chemistry-utils_build.log, #28860

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