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Re: [easychem-devel] crash and backtrace

From: C. <Fra...@en...> - 2006-11-27 22:22:14

> Once in awhile I'll experience a crash and backtrace when creating a
> new molecule, saving it, and then doing File-->New. The original bug
> report is here: https://bugs.gentoo.org/show_bug.cgi?id=156284

>From what I saw in the bug report, the crash doesn't happen with the
binary I provide. Probably the Gentoo package is based on 0.6, while my
binary is based on SVN; a few bugfixes were incorporated to SVN after
0.6. I plan to do a 0.7 release (bugfixes and a few UI changes) near
Christmas.

-- 
FX

[easychem-devel] crash and backtrace

From: Jeffrey G. <jeg...@uh...> - 2006-11-27 22:11:59

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Hash: SHA1

Hello Francois-Xavier,
Once in awhile I'll experience a crash and backtrace when creating a new
 molecule, saving it, and then doing File-->New. The original bug report
is here: https://bugs.gentoo.org/show_bug.cgi?id=156284 , and here is
the crash output:

*** glibc detected *** easychem: double free or corruption (!prev):
0x0000000000731eb0 ***
======= Backtrace: =========
/lib/libc.so.6[0x2b0abf18817e]
/lib/libc.so.6(__libc_free+0x84)[0x2b0abf188304]
/usr/lib/libglib-2.0.so.0(g_free+0x23)[0x2b0abefa7f23]
easychem[0x4086a7]
easychem[0x412523]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x109)[0x2b0abec2d069]
/usr/lib/libgobject-2.0.so.0[0x2b0abec3cf46]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x845)[0x2b0abec3e1e5]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x83)[0x2b0abec3e3c3]
/usr/lib/libgtk-x11-2.0.so.0(gtk_widget_activate+0x6a)[0x2b0abe0da33a]
/usr/lib/libgtk-x11-2.0.so.0(gtk_menu_shell_activate_item+0x100)[0x2b0abdfe9000]
/usr/lib/libgtk-x11-2.0.so.0[0x2b0abdfea4b0]
/usr/lib/libgtk-x11-2.0.so.0[0x2b0abdfdd29d]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x109)[0x2b0abec2d069]
/usr/lib/libgobject-2.0.so.0[0x2b0abec3d0e4]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x613)[0x2b0abec3dfb3]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x83)[0x2b0abec3e3c3]
/usr/lib/libgtk-x11-2.0.so.0[0x2b0abe0d669e]
/usr/lib/libgtk-x11-2.0.so.0(gtk_propagate_event+0xae)[0x2b0abdfd696e]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main_do_event+0x357)[0x2b0abdfd79d7]
/usr/lib/libgdk-x11-2.0.so.0[0x2b0abe36ddbc]
/usr/lib/libglib-2.0.so.0(g_main_context_dispatch+0x1db)[0x2b0abefa1b2b]
/usr/lib/libglib-2.0.so.0[0x2b0abefa234c]
/usr/lib/libglib-2.0.so.0(g_main_loop_run+0x1ad)[0x2b0abefa264d]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main+0xa2)[0x2b0abdfd7d32]
easychem[0x4121f1]
/lib/libc.so.6(__libc_start_main+0xf4)[0x2b0abf137134]
easychem[0x405139]
======= Memory map: ========
00400000-0048c000 r-xp 00000000 08:11 615131
 /usr/bin/easychem
0058c000-0058e000 rw-p 0008c000 08:11 615131
 /usr/bin/easychem
0058e000-007f6000 rw-p 0058e000 00:00 0
 [heap]
2b0abdd8f000-2b0abddac000 r-xp 00000000 08:11 522022
 /lib64/ld-2.4.so
2b0abddac000-2b0abddad000 rw-p 2b0abddac000 00:00 0
2b0abddad000-2b0abddae000 r--p 00000000 08:11 522044
 /usr/lib64/locale/en_US.utf8/LC_IDENTIFICATION
2b0abddae000-2b0abddb5000 r--s 00000000 08:11 6869
 /usr/lib64/gconv/gconv-modules.cache
2b0abddb5000-2b0abddb6000 r--p 00000000 08:11 522043
 /usr/lib64/locale/en_US.utf8/LC_MEASUREMENT
2b0abddb6000-2b0abddb7000 r--p 00000000 08:11 522042
 /usr/lib64/locale/en_US.utf8/LC_TELEPHONE
2b0abddb7000-2b0abddb8000 r--p 00000000 08:11 522041
 /usr/lib64/locale/en_US.utf8/LC_ADDRESS
2b0abddb8000-2b0abddb9000 r--p 00000000 08:11 522040
 /usr/lib64/locale/en_US.utf8/LC_NAME
2b0abddb9000-2b0abddba000 r--p 00000000 08:11 522039
 /usr/lib64/locale/en_US.utf8/LC_PAPER
2b0abddba000-2b0abddbb000 r--p 00000000 08:11 522038
 /usr/lib64/locale/en_US.utf8/LC_MESSAGES/SYS_LC_MESSAGES
2b0abddbb000-2b0abddbc000 r--p 00000000 08:11 522036
 /usr/lib64/locale/en_US.utf8/LC_MONETARY
2b0abddd9000-2b0abddda000 rw-p 2b0abddd9000 00:00 0
2b0abdeab000-2b0abdeac000 r--p 0001c000 08:11 522022
 /lib64/ld-2.4.so
2b0abdeac000-2b0abdead000 rw-p 0001d000 08:11 522022
 /lib64/ld-2.4.so
2b0abdead000-2b0abe21c000 r-xp 00000000 08:11 193788
 /usr/lib64/libgtk-x11-2.0.so.0.1000.6
2b0abe21c000-2b0abe31b000 ---p 0036f000 08:11 193788
 /usr/lib64/libgtk-x11-2.0.so.0.1000.6
2b0abe31b000-2b0abe325000 rw-p 0036e000 08:11 193788
 /usr/lib64/libgtk-x11-2.0.so.0.1000.6
2b0abe325000-2b0abe327000 rw-p 2b0abe325000 00:00 0
2b0abe327000-2b0abe3b6000 r-xp 00000000 08:11 130856
 /usr/lib64/libgdk-x11-2.0.so.0.1000.6
2b0abe3b6000-2b0abe4b5000 ---p 0008f000 08:11 130856
 /usr/lib64/libgdk-x11-2.0.so.0.1000.6
2b0abe4b5000-2b0abe4ba000 rw-p 0008e000 08:11 130856
 /usr/lib64/libgdk-x11-2.0.so.0.1000.6
2b0abe4ba000-2b0abe4d7000 r-xp 00000000 08:11 188954
 /usr/lib64/libatk-1.0.so.0.1211.0
2b0abe4d7000-2b0abe5d6000 ---p 0001d000 08:11 188954
 /usr/lib64/libatk-1.0.so.0.1211.0
2b0abe5d6000-2b0abe5d9000 rw-p 0001c000 08:11 188954
 /usr/lib64/libatk-1.0.so.0.1211.0
2b0abe5d9000-2b0abe5da000 rw-p 2b0abe5d9000 00:00 0
2b0abe5da000-2b0abe5f1000 r-xp 00000000 08:11 129771
 /usr/lib64/libgdk_pixbuf-2.0.so.0.1000.6
2b0abe5f1000-2b0abe6f0000 ---p 00017000 08:11 129771
 /usr/lib64/libgdk_pixbuf-2.0.so.0.1000.6
2b0abe6f0000-2b0abe6f1000 rw-p 00016000 08:11 129771
 /usr/lib64/libgdk_pixbuf-2.0.so.0.1000.6
2b0abe6f1000-2b0abe746000 r-xp 00000000 08:11 522025
 /lib64/libm-2.4.so
2b0abe746000-2b0abe845000 ---p 00055000 08:11 522025
 /lib64/libm-2.4.so
2b0abe845000-2b0abe847000 rw-p 00054000 08:11 522025
 /lib64/libm-2.4.so
2b0abe847000-2b0abe850000 r-xp 00000000 08:11 172761
 /usr/lib64/libpangocairo-1.0.so.0.1201.2
2b0abe850000-2b0abe94f000 ---p 00009000 08:11 172761
 /usr/lib64/libpangocairo-1.0.so.0.1201.2
2b0abe94f000-2b0abe950000 rw-p 00008000 08:11 172761
 /usr/lib64/libpangocairo-1.0.so.0.1201.2
2b0abe950000-2b0abe951000 rw-p 2b0abe950000 00:00 0
2b0abe951000-2b0abe990000 r-xp 00000000 08:11 130424
 /usr/lib64/libpango-1.0.so.0.1201.2
2b0abe990000-2b0abea8f000 ---p 0003f000 08:11 130424
 /usr/lib64/libpango-1.0.so.0.1201.2
2b0abea8f000-2b0abea92000 rw-p 0003e000 08:11 130424
 /usr/lib64/libpango-1.0.so.0.1201.2
2b0abea92000-2b0abeb20000 r-xp 00000000 08:11 193787
 /usr/lib64/libcairo.so.2.9.2
2b0abeb20000-2b0abec1f000 ---p 0008e000 08:11 193787
 /usr/lib64/libcairo.so.2.9.2
2b0abec1f000-2b0abec22000 rw-p 0008d000 08:11 193787
 /usr/lib64/libcairo.so.2.9.2
2b0abec22000-2b0abec64000 r-xp 00000000 08:11 186616
 /usr/lib64/libgobject-2.0.so.0.1200.4
2b0abec64000-2b0abed64000 ---p 00042000 08:11 186616
 /usr/lib64/libgobject-2.0.so.0.1200.4
2b0abed64000-2b0abed66000 rw-p 00042000 08:11 186616
 /usr/lib64/libgobject-2.0.so.0.1200.4
2b0abed66000-2b0abed67000 rw-p 2b0abed66000 00:00 0
2b0abed67000-2b0abed6a000 r-xp 00000000 08:11 186617
 /usr/lib64/libgmodule-2.0.so.0.1200.4
2b0abed6a000-2b0abee69000 ---p 00003000 08:11 186617
 /usr/lib64/libgmodule-2.0.so.0.1200.4
2b0abee69000-2b0abee6a000 rw-p 00002000 08:11 186617
 /usr/lib64/libgmodule-2.0.so.0.1200.4
2b0abee6a000-2b0abee6d000 r-xp 00000000 08:11 522014
 /lib64/libdl-2.4.so
2b0abee6d000-2b0abef6c000 ---p 00003000 08:11 522014
 /lib64/libdl-2.4.so
2b0abef6c000-2b0abef6e000 rw-p 00002000 08:11 522014
 /lib64/libdl-2.4.so
2b0abef6e000-2b0abf018000 r-xp 00000000 08:11 15363
 /usr/lib64/libglib-2.0.so.0.1200.4
2b0abf018000-2b0abf117000 ---p 000aa000 08:11 15363
 /usr/lib64/libglib-2.0.so.0.1200.4
2b0abf117000-2b0abf119000 rw-p 000a9000 08:11 15363
 /usr/lib64/libglib-2.0.so.0.1200.4
2b0abf119000-2b0abf11a000 rw-p 2b0abf119000 00:00 0
2b0abf11a000-2b0abf251000 r-xp 00000000 08:11 522026
 /lib64/libc-2.4.so
2b0abf251000-2b0abf351000 ---p 00137000 08:11 522026
 /lib64/libc-2.4.so
2b0abf351000-2b0abf354000 r--p 00137000 08:11 522026
 /lib64/libc-2.4.so
2b0abf354000-2b0abf356000 rw-p 0013a000 08:11 522026
 /lib64/libc-2.4.so
2b0abf356000-2b0abf35b000 rw-p 2b0abf356000 00:00 0
2b0abf35b000-2b0abf47b000 r-xp 00000000 08:11 3582
 /usr/lib64/libX11.so.6.2.0
2b0abf47b000-2b0abf57b000 ---p 00120000 08:11 3582
 /usr/lib64/libX11.so.6.2.0
2b0abf57b000-2b0abf582000 rw-p 00120000 08:11 3582
 /usr/lib64/libX11.so.6.2.0
2b0abf582000-2b0abf607000 r-xp 00000000 08:11 189020
 /usr/lib64/libfreetype.so.6.3.8
2b0abf607000-2b0abf707000 ---p 00085000 08:11 189020
 /usr/lib64/libfreetype.so.6.3.8
2b0abf707000-2b0abf70c000 rw-p 00085000 08:11 189020
 /usr/lib64/libfreetype.so.6.3.8
2b0abf70c000-2b0abf70d000 rw-p 2b0abf70c000 00:00 0
2b0abf70d000-2b0abf724000 r-xp 00000000 08:11 359714
 /lib64/libz.so.1.2.3
2b0abf724000-2b0abf823000 ---p 00017000 08:11 359714
 /lib64/libz.so.1.2.3
2b0abf823000-2b0abf824000 rw-p 00016000 08:11 359714
 /lib64/libz.so.1.2.3
2b0abf824000-2b0abf85d000 r-xp 00000000 08:11 149303
 /usr/lib64/libfontconfig.so.1.0.4
2b0abf85d000-2b0abf95d000 ---p 00039000 08:11 149303
 /usr/lib64/libfontconfig.so.1.0.4
2b0abf95d000-2b0abf965000 rw-p 00039000 08:11 149303
 /usr/lib64/libfontconfig.so.1.0.4
2b0abf965000-2b0abf967000 rw-p 2b0abf965000 00:00 0
2b0abf967000-2b0abf991000 r-xp 00000000 08:11 129493
 /usr/lib64/libexpat.so.0.5.0
2b0abf991000-2b0abfa91000 ---p 0002a000 08:11 129493
 /usr/lib64/libexpat.so.0.5.0
2b0abfa91000-2b0abfa93000 rw-p 0002a000 08:11 129493
 /usr/lib64/libexpat.so.0.5.0
2b0abfa93000-2b0abfa94000 rw-p 2b0abfa93000 00:00 0
2b0abfa94000-2b0abfaa6000 r-xp 00000000 08:11 130786
 /usr/lib64/libXext.so.6.4.0
2b0abfaa6000-2b0abfba6000 ---p 00012000 08:11 130786
 /usr/lib64/libXext.so.6.4.0
2b0abfba6000-2b0abfba7000 rw-p 00012000 08:11 130786
 /usr/lib64/libXext.so.6.4.0
2b0abfba7000-2b0abfbb0000 r-xp 00000000 08:11 131112
 /usr/lib64/libXrender.so.1.3.0
2b0abfbb0000-2b0abfcaf000 ---p 00009000 08:11 131112
 /usr/lib64/libXrender.so.1.3.0
2b0abfcaf000-2b0abfcb0000 rw-p 00008000 08:11 131112
 /usr/lib64/libXrender.so.1.3.0
2b0abfcb0000-2b0abfcb8000 r-xp 00000000 08:11 150154
 /usr/lib64/libXi.so.6.0.0
2b0abfcb8000-2b0abfdb7000 ---p 00008000 08:11 150154
 /usr/lib64/libXi.so.6.0.0
2b0abfdb7000-2b0abfdb8000 rw-p 00007000 08:11 150154
 /usr/lib64/libXi.so.6.0.0
2b0abfdb8000-2b0abfdb9000 rw-p 2b0abfdb8000 00:00 0
2b0abfdb9000-2b0abfdbc000 r-xp 00000000 08:11 149526
 /usr/lib64/libXrandr.so.2.0.0
2b0abfdbc000-2b0abfebb000 ---p 00003000 08:11 149526
 /usr/lib64/libXrandr.so.2.0.0
2b0abfebb000-2b0abfebc000 rw-p 00002000 08:11 149526
 /usr/lib64/libXrandr.so.2.0.0
2Aborted



Thanks for any help or insight you can provide!

Jeff Gardner
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Re: [easychem-devel] Fonts / Atom Symbols

From: C. <Fra...@en...> - 2006-11-09 12:55:29

> Is there a possibility to "clean" up my molecule? You may know this
> feature from Isis Draw or other programs like that. I like this
> function and it is useful with great molecules and macrocycles.
> 
> And what gives me "clean-up buffer" in the "Transformations" pulldown
> menu?

"Cleanup buffer" detects duplicate bonds (and remove them) and round the
coordinates of all objects, so that objects close to each other will get
the same position.

That's the closest thing you will get to the IsisDraw "clean molecule"
function, but it's far from doing the same thing :)

-- 
FX

Re: [easychem-devel] Fonts / Atom Symbols

From: Wilhelm E. <Wil...@un...> - 2006-11-09 12:20:03

Hello,

> There's a "Bond type" (in the drop-down menu) called "Atom/Group". Yeah,
> it's stupid, but that's the one you want.

Ok. Got it. Another question:

Is there a possibility to "clean" up my molecule? You may know this feature from
Isis Draw or other programs like that. I like this function and it is useful
with great molecules and macrocycles.

And what gives me "clean-up buffer" in the "Transformations" pulldown menu?

I'm really impressed by the output of this little program. By far the best for
drawing molecules on linux.

Great thanks for this.

Greets,

Wilhelm

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Re: [easychem-devel] Fonts / Atom Symbols

From: C. <Fra...@en...> - 2006-11-09 08:54:51

Hi,

> Do I miss something?

Yes, you missed something, but it's actually not so easy to find. It will
be the first thing I change when I have time to work on easychem again.

There's a "Bond type" (in the drop-down menu) called "Atom/Group". Yeah,
it's stupid, but that's the one you want.

FX

[easychem-devel] Fonts / Atom Symbols

From: Wilhelm E. <wil...@un...> - 2006-11-08 13:01:30

Hi there,

I heavily searched the web to find any information about how to draw the
atom symbols (e.g. C, N, Cl ...) in easychem and found nothing. even the
source code doesn't provide any help or howto. Drawing bonds and
changing them, moving them, rotating them and adding ornaments to the
atoms are no problem. I use a recent Gentoo system. Do I miss something?

Cheers,

Wilhelm

Flat | Threaded