Hello, my ubuntu system has coot software installed. It has been running
normally for a long time, but the coot can’t be opened a few days ago. I pasted
the error message below. I don’t know if other additional information is needed.
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/A.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/C.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/G.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/u/U.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DA.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DC.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DG.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DT.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/h/HOH.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/n/NA.cif
Spacegroup: P 1
The program 'coot-bin' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadValue (integer parameter out of range for operation)'.
(Details: serial 347 error_code 2 request_code 151 minor_code 3)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)
. ------ Coot crashed - trying to diagnose -----
ldd -r on guile gives:
linux-vdso.so.1 (0x00007ffde3d76000)
libguile.so.17 => /opt/xtal/ccp4-7.1/libexec/../lib/libguile.so.17
(0x00007f43bcce8000)
libgmp.so.10 => /opt/xtal/ccp4-7.1/libexec/../lib/libgmp.so.10
(0x00007f43bca67000)
libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007f43bca17000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f43bc8c8000)
libltdl.so.7 => /opt/xtal/ccp4-7.1/libexec/../lib/libltdl.so.7
(0x00007f43bc6be000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f43bc69b000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f43bc4a7000)
/lib64/ld-linux-x86-64.so.2 (0x00007f43bcfec000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f43bc4a1000)
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007,
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well. For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
Gtk-Message: Failed to load module "gail"
Gtk-Message: Failed to load module "atk-bridge"
Gtk-Message: Failed to load module "canberra-gtk-module"
coot-exe: "/opt/xtal/ccp4-7.1/libexec/coot-bin"
/usr/bin/ls
-rwxr-xr-x 1 root root 9169416 Oct 18 22:22 /opt/xtal/ccp4-7.1/libexec/coot-bin
coot-version:
/opt/xtal/ccp4-7.1/libexec/coot-bin
Builder_info: CCP4, Oxfordshire
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas
GSL SQLite3 LibCurl
Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
git commit: 0b823e493e00c1199103369ddab6641e14560d00
Builder_info: CCP4, Oxfordshire
[with python 2.7.16 embedded]
[with guile 1.8.8 embedded]
0.9.6 (revision-count 10625)
platform:
/usr/bin/uname
Linux gaolab-DELL 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10
UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
core: #f
No core file found. No debugging
0.9.6 (revision-count 10625)
[with guile 1.8.8 embedded]
[with python 2.7.16 embedded]
Builder_info: CCP4, Oxfordshire
git commit: 0b823e493e00c1199103369ddab6641e14560d00
Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas
GSL SQLite3 LibCurl
Builder_info: CCP4, Oxfordshire
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