[COOT] Latest Coot from Fink crashing
Dear all, After upgrading to latest (Fink's 0.7.1-pre-4562) coot we are experiencing a strange problem: coot reproducibly crashes if one tries to centre on a non-protein non-water atom. Coot's last words: (0) " S "/1/chainid="B"/1/DMS, occ: 0.79 with B-factor: 27.78 element: " S" at (12.282,65.946,153.1) : 0.180006 INFO:: recentre: clicked on imol: 0 coot-real(60501,0x7fff71290cc0) malloc: *** error for object 0x7fff5fbfbd68: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug /sw/bin/coot: line 6: 60501 Abort trap /sw/bin/coot-real "$@" or (0) " P "/1/chainid=""/1/PO4, occ: 1 with B-factor: 30 element: " P" at (0,0.021,0.036) : 0.153325 INFO:: recentre: clicked on imol: 0 coot-real(19455,0x7fff70f8dcc0) malloc: *** error for object 0x7fff5fbfbea8: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug /sw/bin/coot: line 6: 19455 Abort trap /sw/bin/coot-real "$@" every time it's something about "pointer being freed was not allocated". Purging and rebuilding Coot does not fix the problem. Has anybody seen this behaviour? Best regards, Dmitry
Re: [COOT] Latest Coot from Fink crashing
This seems to be a 10.6 issue since same version on 10.8 centres fine. On 2013-02-19, at 4:09 PM, Dmitry Rodionov wrote: > Dear all, > > After upgrading to latest (Fink's 0.7.1-pre-4562) coot we are experiencing a > strange problem: > coot reproducibly crashes if one tries to centre on a non-protein non-water > atom. > > Coot's last words: > > (0) " S "/1/chainid="B"/1/DMS, occ: 0.79 with B-factor: 27.78 element: " S" > at (12.282,65.946,153.1) : 0.180006 > INFO:: recentre: clicked on imol: 0 > coot-real(60501,0x7fff71290cc0) malloc: *** error for object 0x7fff5fbfbd68: > pointer being freed was not allocated > *** set a breakpoint in malloc_error_break to debug > /sw/bin/coot: line 6: 60501 Abort trap /sw/bin/coot-real "$@" > > or > > (0) " P "/1/chainid=""/1/PO4, occ: 1 with B-factor: 30 element: " P" at > (0,0.021,0.036) : 0.153325 > INFO:: recentre: clicked on imol: 0 > coot-real(19455,0x7fff70f8dcc0) malloc: *** error for object 0x7fff5fbfbea8: > pointer being freed was not allocated > *** set a breakpoint in malloc_error_break to debug > /sw/bin/coot: line 6: 19455 Abort trap /sw/bin/coot-real "$@" > > every time it's something about "pointer being freed was not allocated". > > Purging and rebuilding Coot does not fix the problem. > > Has anybody seen this behaviour? > > Best regards, > Dmitry >
Re: [COOT] Latest Coot from Fink crashing
Sorry. I just got my 10.6 computer back up and did another build a few hours ago. I haven't been able to reproduce the issue, but was only trying on 10.8. I'm having python mis-match problems on 10.6. On Feb 19, 2013, at 7:21 PM, Dmitry Rodionov wrote: > This seems to be a 10.6 issue since same version on 10.8 centres fine. > > On 2013-02-19, at 4:09 PM, Dmitry Rodionov wrote: > >> Dear all, >> >> After upgrading to latest (Fink's 0.7.1-pre-4562) coot we are experiencing a >> strange problem: >> coot reproducibly crashes if one tries to centre on a non-protein non-water >> atom. >> >> Coot's last words: >> >> (0) " S "/1/chainid="B"/1/DMS, occ: 0.79 with B-factor: 27.78 element: " >> S" at (12.282,65.946,153.1) : 0.180006 >> INFO:: recentre: clicked on imol: 0 >> coot-real(60501,0x7fff71290cc0) malloc: *** error for object 0x7fff5fbfbd68: >> pointer being freed was not allocated >> *** set a breakpoint in malloc_error_break to debug >> /sw/bin/coot: line 6: 60501 Abort trap /sw/bin/coot-real "$@" >> >> or >> >> (0) " P "/1/chainid=""/1/PO4, occ: 1 with B-factor: 30 element: " P" at >> (0,0.021,0.036) : 0.153325 >> INFO:: recentre: clicked on imol: 0 >> coot-real(19455,0x7fff70f8dcc0) malloc: *** error for object 0x7fff5fbfbea8: >> pointer being freed was not allocated >> *** set a breakpoint in malloc_error_break to debug >> /sw/bin/coot: line 6: 19455 Abort trap /sw/bin/coot-real "$@" >> >> every time it's something about "pointer being freed was not allocated". >> >> Purging and rebuilding Coot does not fix the problem. >> >> Has anybody seen this behaviour? >> >> Best regards, >> Dmitry >>
Re: [COOT] Latest Coot from Fink crashing
On 20/02/13 03:33, William G. Scott wrote: Sorry. I just got my 10.6 computer back up and did another build a few hours ago. I haven't been able to reproduce the issue, but was only trying on 10.8. OK I'm having python mis-match problems on 10.6. :-( that was the only thing that I could think of... Paul.
Re: [COOT] Latest Coot from Fink crashing
Is there anything I can do about it? other than upgrading to 10.8 ) Can regular coot binaries be installed in /usr/local on OS X ? Dmitry On 2013-02-27, at 11:39 AM, Paul Emsley wrote: > On 20/02/13 03:33, William G. Scott wrote: >> Sorry. I just got my 10.6 computer back up and did another build a few >> hours ago. >> >> I haven't been able to reproduce the issue, but was only trying on 10.8. > > OK >> >> I'm having python mis-match problems on 10.6. >> >> > > :-( that was the only thing that I could think of... > > Paul.
