Bug: fatal error with notmuch new, second run starts indexing all over again

Gregor Zattler telegraph at gmx.net
Thu Jul 6 02:31:01 PDT 2017


Hi David, notmuch developers,
* David Bremner <david at tethera.net> [03. Jul. 2017]:
> Try setting a break in _notmuch_database_log (b _notmuch_database_log)
> and run "bt" at that break point. It might (or might not) be worth
> continuing after the first breakpoint to inspect other errors.

I did so with newest notmuch:

0 (master *) grfz at len:~/tmp$ notmuch --version
notmuch 0.24.2+84~g1ec6344
0 (master *) grfz at len:~/tmp$

0 (master=) grfz at len:~/src/notmuch$ gdb --args /home/grfz/src/notmuch/notmuch new
GNU gdb (Debian 7.12-6) 7.12.0.20161007-git
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /home/grfz/src/notmuch/notmuch...done.
(gdb) b _notmuch_database_log
Breakpoint 1 at 0x1f6e0: file lib/database.cc, line 426.
(gdb) run
Starting program: /home/grfz/src/notmuch/notmuch new
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Found 941498 total files (that's not much mail).
q
Breakpoint 1, _notmuch_database_log (notmuch=0x555555825dd0, format=0x55555558d258 "A Xapian exception occurred adding message: %s.\n") at lib/database.cc:426
426     {
(gdb) bt
#0  _notmuch_database_log (notmuch=0x555555825dd0, format=0x55555558d258 "A Xapian exception occurred adding message: %s.\n") at lib/database.cc:426
#1  0x0000555555577f58 in notmuch_database_add_message (notmuch=notmuch at entry=0x555555825dd0, filename=filename at entry=0x55557b204400 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org/cur/1488666048.R6065357166258349555.len:2,",
    message_ret=message_ret at entry=0x7fffffffd048) at lib/database.cc:2597
#2  0x000055555556802f in add_file (state=0x7fffffffd540, filename=0x55557b204400 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org/cur/1488666048.R6065357166258349555.len:2,", notmuch=0x555555825dd0) at notmuch-new.c:264
#3  add_files (notmuch=notmuch at entry=0x555555825dd0, path=path at entry=0x555574a15b80 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org/cur", state=state at entry=0x7fffffffd540) at notmuch-new.c:599
#4  0x0000555555567b44 in add_files (notmuch=notmuch at entry=0x555555825dd0, path=path at entry=0x55558520f1b0 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org", state=state at entry=0x7fffffffd540) at notmuch-new.c:483
#5  0x0000555555567b44 in add_files (notmuch=notmuch at entry=0x555555825dd0, path=path at entry=0x5555638993b0 "/home/grfz/Mail/~ml", state=state at entry=0x7fffffffd540) at notmuch-new.c:483
#6  0x0000555555567b44 in add_files (notmuch=0x555555825dd0, path=path at entry=0x5555557cf710 "/home/grfz/Mail", state=state at entry=0x7fffffffd540) at notmuch-new.c:483
#7  0x00005555555689ed in notmuch_new_command (config=0x5555557ce1d0, argc=<optimized out>, argv=<optimized out>) at notmuch-new.c:1099
#8  0x0000555555561a27 in main (argc=<optimized out>, argv=0x7fffffffda68) at notmuch.c:456
(gdb) continue
Continuing.
Error: A Xapian exception occurred. Halting processing.
Processed 660118 total files in 8h 59m 43s (20 files/sec.).
Added 584749 new messages to the database.
Note: A fatal error was encountered: A Xapian exception occurred
[Inferior 1 (process 14593) exited with code 01]
(gdb) continue
The program is not being run.
(gdb)



Since the gdb output shows a filename I looked at its contents:
There is a second "Content-Length:" -Header which does not make
sense but otherwise should not be a problem.  

Since its an email from an open mailing list I attach it to
this very email.

I then configured notmuch to scan the whole mail folder
/home/grfz/Mail/~ml/emacs-orgmode at gnu.org: 

0 (master=) grfz at len:~/src/notmuch$ gdb --args /home/grfz/src/notmuch/notmuch new
GNU gdb (Debian 7.12-6) 7.12.0.20161007-git
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /home/grfz/src/notmuch/notmuch...done.
(gdb) b _notmuch_database_log
Breakpoint 1 at 0x1f6e0: file lib/database.cc, line 426.
(gdb) run
Starting program: /home/grfz/src/notmuch/notmuch new
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Found 114424 total files (that's not much mail).

Breakpoint 1, _notmuch_database_log (notmuch=0x5555557d2780, format=0x55555558d258 "A Xapian exception occurred adding message: %s.\n") at lib/database.cc:426
426     {
(gdb) bt
#0  _notmuch_database_log (notmuch=0x5555557d2780, format=0x55555558d258 "A Xapian exception occurred adding message: %s.\n") at lib/database.cc:426
#1  0x0000555555577f58 in notmuch_database_add_message (notmuch=notmuch at entry=0x5555557d2780, filename=filename at entry=0x555558118ba0 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org/cur/1488666090.R8081408151026683680.len:2,",
    message_ret=message_ret at entry=0x7fffffffd2c8) at lib/database.cc:2597
#2  0x000055555556802f in add_file (state=0x7fffffffd540, filename=0x555558118ba0 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org/cur/1488666090.R8081408151026683680.len:2,", notmuch=0x5555557d2780) at notmuch-new.c:264
#3  add_files (notmuch=notmuch at entry=0x5555557d2780, path=path at entry=0x5555557d25f0 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org/cur", state=state at entry=0x7fffffffd540) at notmuch-new.c:599
#4  0x0000555555567b44 in add_files (notmuch=0x5555557d2780, path=path at entry=0x5555557d4f90 "/home/grfz/Mail/~ml/emacs-orgmode at gnu.org", state=state at entry=0x7fffffffd540) at notmuch-new.c:483
#5  0x00005555555689ed in notmuch_new_command (config=0x5555557ce1d0, argc=<optimized out>, argv=<optimized out>) at notmuch-new.c:1099
#6  0x0000555555561a27 in main (argc=<optimized out>, argv=0x7fffffffda68) at notmuch.c:456
(gdb) continue
Continuing.
Error: A Xapian exception occurred. Halting processing.
Processed 69364 total files in 24m 51s (46 files/sec.).
Added 69350 new messages to the database.
Note: A fatal error was encountered: A Xapian exception occurred
[Inferior 1 (process 23253) exited with code 01]
(gdb) continue
The program is not being run.
(gdb)


--> This time it's another file with another email but at closer
inspection it shows it also has two "Content-Length:" -headers.  For
the sake of consistency I attach the file to this very email.


I then created a test maildir folder with the first offending email as
the very only email and configured notmuch to only scan this test
maildir folder: *no problem*.  I the put the second offending email in
the test maildir folder and tried again: *no problem*



I then rescanned the maildir folder with emacs-org-mode mailing list
emails with notmuch from debian stretch:
0 (master=) grfz at len:~/src/notmuch$ rm -rf /home/grfz/Mail/~ml/emacs-orgmode at gnu.org/.notmuch/
0 (master=) grfz at len:~/src/notmuch$ gdb --args /usr/bin/notmuch new
GNU gdb (Debian 7.12-6) 7.12.0.20161007-git
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show
copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /usr/bin/notmuch...(no debugging symbols
found)...done.
(gdb) b _notmuch_database_log
Function "_notmuch_database_log" not defined.
Make breakpoint pending on future shared library load? (y or [n]) y
Breakpoint 1 (_notmuch_database_log) pending.
(gdb) run
Starting program: /usr/bin/notmuch new
[Thread debugging using libthread_db enabled]
Using host libthread_db library
"/lib/x86_64-linux-gnu/libthread_db.so.1".
Found 114424 total files (that's not much mail).
Error: A Xapian exception occurred. Halting processing.
Processed 69364 total files in 13m 45s (84 files/sec.).
Added 69350 new messages to the database.
Note: A fatal error was encountered: A Xapian exception occurred
[Inferior 1 (process 24459) exited with code 01]
(gdb) bt
No stack.
(gdb) continue
The program is not being run.
(gdb)




Since notmuch from debian strech also produced a xapian exeption I
assume bisecting will be of no help.  I'll try to bisect but the next
week or so I don't have much free time.  I also will run memtest and
smartmontools.


Thanks for your help, Gregor
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To: "Thomas S. Dye" <tsd at tsdye.com>
From: Nick Dokos <nicholas.dokos at hp.com>
Subject: Re: [O] LaTeX export: inline markup underscore problem
In-reply-to: Message from "Thomas S. Dye" <tsd at tsdye.com> of
	"Sun, 10 Apr 2011 09:36:35 -1000."
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Thomas S. Dye <tsd at tsdye.com> wrote:

> Aloha Mauro,
> 
> Please see
> 
> http://orgmode.org/worg/org-tutorials/org-latex-export.html#sec-17_2
> 

Excuse the intrusion, but I don't see anything in there that looks like
a solution to the OP's problem (the undesired quoting of the underscore
when exporting the org file to LaTeX): what am I missing?

I was going to suggest that life would be much easier for the OP if he
could change all underscores to some other character in his bibliography
(I often see colons and minus signs used e.g.) That may or may not be
possible of course, but if it is possible, it would be the simplest
solution: the treatment of _ in the LaTeX exporter is often the source
of frustration. That is not the fault of the exporter of course: TeX
makes it very complicated to determine what the right thing to do is.

Nick




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Nick Dokos <nicholas.dokos at hp.com> wrote:

> Nicolas Goaziou <n.goaziou at gmail.com> wrote:
> 
> > Hello,
> > 
> > Marvin Doyley <marvinpas at gmail.com> writes:
> > 
> > > I use to use C-c - to convert headlines to plain list, but for some reason
> > > when I do this it tries to make a table of content, see below
> > >
> > > TABLE-OF-CONTENTS on ~/Documents/General/O/org/planner.org
> > > SPC=view TAB=goto RET=goto+hide [q]uit [r]escan [l]abels [f]ollow [x]r
> > > [?]Help
> > 
> > I cannot reproduce this. Could you be more explicit ? What is your test
> > file, where do you have cursor when you use C-c -, etc.
> > 
> 
> It looks as if C-c - has been remapped by some package. What does C-h k
> say for it? What minor modes are in effect in the planner.org buffer?
> Maybe if you ask for Help with ? in the context above, it'll give
> you an idea of who it is that's doing this.
> 

Looks like reftex is the culprit - you can blame the guy who created
reftex, what's his name? Ah, yes: Carsten Dominik :-)

But why do you have reftex turned on in an org buffer?

Nick





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