To whom it may concern,
Recently, I have a problem with coot after Ubuntu upgrade from 18.04 to 20.04.
I could not launch the coot as it showed the message below. May I know what is
going wrong with the software?
Thanks for the help.
Best regards
HK
coot-bin:4860): GLib-GObject-WARNING **: 12:03:32.714:
g_object_set_is_valid_property: object class 'GtkSettings' has no property
named 'gtk-application-prefer-dark-theme'
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/
There are 166 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/a/ALA.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/a/ASP.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/a/ASN.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/c/CYS.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/g/GLN.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/g/GLY.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/g/GLU.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/p/PHE.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/h/HIS.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/i/ILE.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/l/LYS.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/l/LEU.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/m/MET.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/m/MSE.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/p/PRO.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/a/ARG.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/s/SER.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/t/THR.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/v/VAL.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/t/TRP.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/t/TYR.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/p/PO4.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/s/SO4.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/g/GOL.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/c/CIT.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/e/EDO.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/a/A.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/c/C.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/g/G.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/u/U.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/d/DA.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/d/DC.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/d/DG.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/d/DT.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/h/HOH.cif
There are 2 data in
/home/mauricetam/Documents/software/ccp4-7.1/ccp4-7.1/lib/data/monomers/n/NA.cif
Spacegroup: P 1
libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot
open shared object file: No such file or directory (search paths
/usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot
open shared object file: No such file or directory (search paths
/usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so:
cannot open shared object file: No such file or directory (search paths
/usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri)
libGL error: failed to load driver: swrast
(coot-bin:4860): GtkGLExt-WARNING **: 12:03:33.432: cannot create GdkGLContext
(coot-bin:4860): GdkGLExt-CRITICAL **: 12:03:33.432:
gdk_gl_window_impl_x11_make_context_current: assertion
'GDK_IS_GL_CONTEXT_IMPL_X11 (glcontext)' failed
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 368 error_code 2 request_code 152 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 (0x00007ffcc0f3c000)
libguile.so.17 =>
/home/mauricetam/Documents/software/coot/lib/libguile.so.17 (0x00007ff7c1af7000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007ff7c1aa4000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff7c18b2000)
libgmp.so.10 =>
/home/mauricetam/Documents/software/coot/lib/libgmp.so.10 (0x00007ff7c163b000)
libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1
(0x00007ff7c1600000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff7c14af000)
libltdl.so.3 =>
/home/mauricetam/Documents/software/coot/lib/libltdl.so.3 (0x00007ff7c12a7000)
/lib64/ld-linux-x86-64.so.2 (0x00007ff7c1def000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007ff7c12a1000)
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:
coot-exe: "/home/mauricetam/Documents/software/coot/libexec/coot-bin"
/bin/ls
coot-version:
/home/mauricetam/Documents/software/coot/libexec/coot-bin
platform:
/bin/uname
core: #f
No core file found. No debugging
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