Open Babel / Bugs / #575 crash when converting a CIF file

crash when converting a CIF file

#575 crash when converting a CIF file

Milestone: 2.3.x

Status: closed

Owner: Geoff Hutchison

Labels: Command-line Tools (114)

Priority: 5

Updated: 2015-02-17

Created: 2010-01-05

Creator: Anonymous

Private: No

The attached CIF file makes OpenBabel crashs either if used as a library or using the command-line convertion tool.

This appends on a Debian sid with OpenBabel 2.2.3 or on an Ubuntu Hardy with 2.1.1. The message is:

caliste@myrte:~/tmp$ babel Open_babel_crash.cif *** glibc detected *** babel: double free or ======= Backtrace: =========
/lib/libc.so.6[0x7f392848008a]
/lib/libc.so.6(cfree+0x8c)[0x7f3928483c1c]ZN9OpenBabel5OBMol14C /usr/lib/openbabel/2.1/cifformat.so(_ZN9OpenBabel9CI /usr/lib/openbabel/2.1/cifformat.so(_ZN9OpenBabel16O /usr/lib/openbabel/2.1/cifformat.so(_ZN9OpenBabel16O /usr/lib/libopenbabel.so.2(_ZN9OpenBabel12OBConversi /usr/lib/libopenbabel.so.2(_ZN9OpenBabel12OBConversi /usr/lib/libopenbabel.so.2(_ZN9OpenBabel12OBConversi babel[0x402f26]
/lib/libc.so.6(__libc_start_main+0xf4)[0x7f392 babel(__gxx_personality_v0+0x81)[0x401de9] 00400000-00406000 r-xp 00000000 08:01 70139 00605000-00606000 rw-p 00005000 08:01 70139 00606000-006c1000 rw-p 00606000 00:00 0 7f3918000000-7f3918021000 rw-p 7f3918000000 7f3918021000-7f391c000000 ---p 7f3918021000 7f391f391000-7f391f3a1000 r-xp 00000000 08:01 920605 7f391f3a1000-7f391f5a1000 ---p 00010000 08:01 920605 7f391f5a1000-7f391f5a2000 rw-p 00010000 08:01 920605 7f391f5a2000-7f391f5b2000 r-xp 00000000 08:01 920650 7f391f5b2000-7f391f7b2000 ---p 00010000 08:01 920650 7f391f7b2000-7f391f7b3000 rw-p 00010000 08:01 920650 7f391f7b3000-7f391f7c1000 r-xp 00000000 08:01 920588 7f391f7c1000-7f391f9c1000 ---p 0000e000 08:01 920588 7f391f9c1000-7f391f9c2000 rw-p 0000e000 08:01 920588 7f391f9c2000-7f391f9cf000 r-xp 00000000 08:01 920606 7f391f9cf000-7f391fbcf000 ---p 0000d000 08:01 920606 7f391fbcf000-7f391fbd0000 rw-p 0000d000 08:01 920606 7f391fbd0000-7f391fbdf000 r-xp 00000000 08:01 920631 7f391fbdf000-7f391fdde000 ---p 0000f000 08:01 920631 7f391fdde000-7f391fddf000 rw-p 0000e000 08:01 920631 7f391fddf000-7f391fe02000 r-xp 00000000 08:01 920602 7f391fe02000-7f3920002000 ---p 00023000 08:01 920602 7f3920002000-7f3920003000 rw-p 00023000 08:01 920602 7f3920003000-7f39200f6000 r-xp 00000000 08:01 920621 7f39200f6000-7f39202f6000 ---p 000f3000 08:01 920621 7f39202f6000-7f39202fa000 rw-p 000f3000 08:01 920621 7f39202fa000-7f3920308000 r-xp 00000000 08:01 920612 7f3920308000-7f3920507000 ---p 0000e000 08:01 920612 7f3920507000-7f3920508000 rw-p 0000d000 08:01 920612 7f3920508000-7f392050b000 r-xp 00000000 08:01 920587 7f392050b000-7f392070a000 ---p 00003000 08:01 920587 7f392070a000-7f392070b000 rw-p 00002000 08:01 920587 7f392070b000-7f3920721000 r-xp 00000000 08:01 920593 7f3920721000-7f3920921000 ---p 00016000 08:01 920593 7f3920921000-7f3920922000 rw-p 00016000 08:01 920593 7f3920922000-7f3920931000 r-xp 00000000 08:01 920590 7f3920931000-7f3920b30000 ---p 0000f000 08:01 920590 7f3920b30000-7f3920b31000 rw-p 0000e000 08:01 920590 7f3920b31000-7f3920b43000 r-xp 00000000 08:01 920627 7f3920b43000-7f3920d42000 ---p 00012000 08:01 920627 7f3920d42000-7f3920d43000 rw-p 00011000 08:01 920627 7f3920d43000-7f3920d51000 r-xp 00000000 08:01 920622 7f3920d51000-7f3920f51000 ---p 0000e000 08:01 920622 7f3920f51000-7f3920f52000 rw-p 0000e000 08:01 920622 7f3920f52000-7f3920f60000 r-xp 00000000 08:01 920584 7f3920f60000-7f3921160000 ---p 0000e000 08:01 920584 7f3921160000-7f3921161000 rw-p 0000e000 08:01 920584 7f3921161000-7f392116f000 r-xp 00000000 08:01 920608 7f392116f000-7f392136f000 ---p 0000e000 08:01 920608 7f392136f000-7f3921370000 rw-p 0000e000 08:01 920608 7f3921370000-7f3921385000 r-xp 00000000 08:01 920603 7f3921385000-7f3921585000 ---p 00015000 08:01 920603 7f3921585000-7f3921586000 rw-p 00015000 08:01 920603 7f3921586000-7f3921593000 r-xp 00000000 08:01 920619 7f3921593000-7f3921793000 ---p 0000d000 08:01 920619 7f3921793000-7f3921794000 rw-p 0000d000 08:01 920619 7f3921794000-7f39217a1000 r-xp 00000000 08:01 920643 7f39217a1000-7f39219a1000 ---p 0000d000 08:01 920643 7f39219a1000-7f39219a2000 rw-p 0000d000 08:01 920643 7f39219a2000-7f39219b1000 r-xp 00000000 08:01 920597 7f39219b1000-7f3921bb1000 ---p 0000f000 08:01 920597 7f3921bb1000-7f3921bb2000 rw-p 0000f000 08:01 920597 7f3921bb2000-7f3921bc0000 r-xp 00000000 08:01 920594 7f3921bc0000-7f3921dbf000 ---p 0000e000 08:01 920594 7f3921dbf000-7f3921dc0000 rw-p 0000d000 08:01 920594 7f3921dc0000-7f3921dce000 r-xp 00000000 08:01 920630 7f3921dce000-7f3921fce000 ---p 0000e000 08:01 920630 7f3921fce000-7f3921fcf000 rw-p 0000e000 08:01 920630 7f3921fcf000-7f3921fe0000 r-xp 00000000 08:01 920633 7f3921fe0000-7f39221e0000 ---p 00011000 08:01 920633 7f39221e0000-7f39221e1000 rw-p 00011000 08:01 920633 7f39221e1000-7f39221e3000 r-xp 00000000 08:01 920604 7f39221e3000-7f39223e3000 ---p 00002000 08:01 920604 7f39223e3000-7f39223e4000 rw-p 00002000 08:01 920604 7f39223e4000-7f39223f2000 r-xp 00000000 08:01 920628 7f39223f2000-7f39225f2000 ---p 0000e000 08:01 920628 7f39225f2000-7f39225f3000 rw-p 0000e000 08:01 920628 7f39225f3000-7f3922601000 r-xp 00000000 08:01 920586 7f3922601000-7f3922800000 ---p 0000e000 08:01 920586 7f3922800000-7f3922801000 rw-p 0000d000 08:01 920586 7f3922801000-7f3922811000 r-xp 00000000 08:01 920641 7f3922811000-7f3922a11000 ---p 00010000 08:01 920641 7f3922a11000-7f3922a12000 rw-p 00010000 08:01 920641 7f3922a12000-7f3922a27000 r-xp 00000000 08:01 920632 7f3922a27000-7f3922c26000 ---p 00015000 08:01 920632 7f3922c26000-7f3922c27000 rw-p 00014000 08:01 920632 7f3922c27000-7f3922c35000 r-xp 00000000 08:01 920629 7f3922c35000-7f3922e35000 ---p 0000e000 08:01 920629 7f3922e35000-7f3922e36000 rw-p 0000e000 08:01 920629 7f3922e36000-7f3922e44000 r-xp 00000000 08:01 920620 7f3922e44000-7f3923044000 ---p 0000e000 08:01 920620 7f3923044000-7f3923045000 rw-p 0000e000 08:01 920620 7f3923045000-7f3923052000 r-xp 00000000 08:01 920613 7f3923052000-7f3923252000 ---p 0000d000 08:01 920613 7f3923252000-7f3923253000 rw-p 0000d000 08:01 920613 7f3923253000-7f3923262000 r-xp 00000000 08:01 920637 7f3923262000-7f3923462000 ---p 0000f000 08:01 920637 7f3923462000-7f3923463000 rw-p 0000f000 08:01 920637 7f3923463000-7f3923471000 r-xp 00000000 08:01 920614 7f3923471000-7f3923671000 ---p 0000e000 08:01 920614 7f3923671000-7f3923672000 rw-p 0000e000 08:01 920614 7f3923672000-7f3923682000 r-xp 00000000 08:01 920624 7f3923682000-7f3923882000 ---p 00010000 08:01 920624 7f3923882000-7f3923883000 rw-p 00010000 08:01 920624 7f3923883000-7f392389c000 r-xp 00000000 08:01 920623 7f392389c000-7f3923a9c000 ---p 00019000 08:01 920623 7f3923a9c000-7f3923a9d000 rw-p 00019000 08:01 920623 7f3923a9d000-7f3923aab000 r-xp 00000000 08:01 920585 7f3923aab000-7f3923cab000 ---p 0000e000 08:01 920585 7f3923cab000-7f3923cac000 rw-p 0000e000 08:01 920585 7f3923cac000-7f3923cba000 r-xp 00000000 08:01 920626 7f3923cba000-7f3923eb9000 ---p 0000e000 08:01 920626 7f3923eb9000-7f3923eba000 rw-p 0000d000 08:01 920626 7f3923eba000-7f3923ebf000 r-xp 00000000 08:01 920638 7f3923ebf000-7f39240be000 ---p 00005000 08:01 920638 7f39240be000-7f39240bf000 rw-p 00004000 08:01 920638 7f39240bf000-7f39240cf000 r-xp 00000000 08:01 920591 7f39240cf000-7f39242ce000 ---p 00010000 08:01 920591 7f39242ce000-7f39242cf000 rw-p 0000f000 08:01 920591 7f39242cf000-7f39242df000 r-xp 00000000 08:01 920617 7f39242df000-7f39244df000 ---p 00010000 08:01 920617 7f39244df000-7f39244e0000 rw-p 00010000 08:01 920617 7f39244e0000-7f39244ef000 r-xp 00000000 08:01 920636 7f39244ef000-7f39246ef000 ---p 0000f000 08:01 920636 7f39246ef000-7f39246f0000 rw-p 0000f000 08:01 920636 7f39246f0000-7f3924702000 r-xp 00000000 08:01 920635 7f3924702000-7f3924902000 ---p 00012000 08:01 920635 7f3924902000-7f3924903000 rw-p 00012000 08:01 920635 7f3924903000-7f3924913000 r-xp 00000000 08:01 920648 7f3924913000-7f3924b13000 ---p 00010000 08:01 920648 7f3924b13000-7f3924b14000 rw-p 00010000 08:01 920648 7f3924b14000-7f3924b24000 r-xp 00000000 08:01 920634 7f3924b24000-7f3924d24000 ---p 00010000 08:01 920634 7f3924d24000-7f3924d25000 rw-p 00010000 08:01 920634 7f3924d25000-7f3924d42000 r-xp 00000000 08:01 920640 7f3924d42000-7f3924f42000 ---p 0001d000 08:01 920640 7f3924f42000-7f3924f43000 rw-p 0001d000 08:01 920640 7f3924f43000-7f3924f51000 r-xp 00000000 08:01 920592 7f3924f51000-7f3925150000 ---p 0000e000 08:01 920592 7f3925150000-7f3925151000 rw-p 0000d000 08:01 920592 7f3925151000-7f392515f000 r-xp 00000000 08:01 920607 7f392515f000-7f392535e000 ---p 0000e000 08:01 920607 7f392535e000-7f392535f000 rw-p 0000d000 08:01 920607 7f392535f000-7f392536d000 r-xp 00000000 08:01 920651 7f392536d000-7f392556c000 ---p 0000e000 08:01 920651 7f392556c000-7f392556d000 rw-p 0000d000 08:01 920651 7f392556d000-7f392557b000 r-xp 00000000 08:01 920600 7f392557b000-7f392577a000 ---p 0000e000 08:01 920600 7f392577a000-7f392577b000 rw-p 0000d000 08:01 920600 7f392577b000-7f3925789000 r-xp 00000000 08:01 920646 7f3925789000-7f3925988000 ---p 0000e000 08:01 920646 7f3925988000-7f3925989000 rw-p 0000d000 08:01 920646 7f3925989000-7f3925997000 r-xp 00000000 08:01 920599 7f3925997000-7f3925b96000 ---p 0000e000 08:01 920599 7f3925b96000-7f3925b97000 rw-p 0000d000 08:01 920599 7f3925b97000-7f3925ba5000 r-xp 00000000 08:01 920645 7f3925ba5000-7f3925da4000 ---p 0000e000 08:01 920645 7f3925da4000-7f3925da5000 rw-p 0000d000 08:01 920645 7f3925da5000-7f3925db3000 r-xp 00000000 08:01 920609 7f3925db3000-7f3925fb3000 ---p 0000e000 08:01 920609 7f3925fb3000-7f3925fb4000 rw-p 0000e000 08:01 920609 7f3925fb4000-7f3925fc5000 r-xp 00000000 08:01 920625 7f3925fc5000-7f39261c5000 ---p 00011000 08:01 920625 7f39261c5000-7f39261c6000 rw-p 00011000 08:01 920625 7f39261c6000-7f39261d3000 r-xp 00000000 08:01 920647 7f39261d3000-7f39263d3000 ---p 0000d000 08:01 920647 7f39263d3000-7f39263d4000 rw-p 0000d000 08:01 920647 7f39263d4000-7f39263e7000 r-xp 00000000 08:01 920598 7f39263e7000-7f39265e7000 ---p 00013000 08:01 920598 7f39265e7000-7f39265e8000 rw-p 00013000 08:01 920598 7f39265e8000-7f3926608000 r-xp 00000000 08:01 920601 7f3926608000-7f3926808000 ---p 00020000 08:01 920601 7f3926808000-7f3926809000 rw-p 00020000 08:01 920601 7f3926809000-7f3926818000 r-xp 00000000 08:01 920649 7f3926818000-7f3926a18000 ---p 0000f000 08:01 920649 7f3926a18000-7f3926a19000 rw-p 0000f000 08:01 920649 7f3926a19000-7f3926a26000 r-xp 00000000 08:01 920642 7f3926a26000-7f3926c26000 ---p 0000d000 08:01 920642 7f3926c26000-7f3926c27000 rw-p 0000d000 08:01 920642 7f3926c27000-7f3926c30000 r-xp 00000000 08:01 920610 7f3926c30000-7f3926e30000 ---p 00009000 08:01 920610 7f3926e30000-7f3926e31000 rw-p 00009000 08:01 920610 7f3926e31000-7f3926f6e000 r-xp 00000000 08:01 66586 7f3926f6e000-7f392716e000 ---p 0013d000 08:01 66586 7f392716e000-7f3927177000 rw-p 0013d000 08:01 66586 7f3927177000-7f3927178000 rw-p 7f3927177000 7f3927178000-7f392718c000 r-xp 00000000 08:01 920596 7f392718c000-7f392738b000 ---p 00014000 08:01 920596 7f392738b000-7f392738c000 rw-p 00013000 08:01 920596 7f392738c000-7f392739e000 r-xp 00000000 08:01 920611 7f392739e000-7f392759d000 ---p 00012000 08:01 920611 7f392759d000-7f392759e000 rw-p 00011000 08:01 920611 7f392759e000-7f39275ad000 r-xp 00000000 08:01 920615 7f39275ad000-7f39277ad000 ---p 0000f000 08:01 920615 7f39277ad000-7f39277ae000 rw-p 0000f000 08:01 920615 7f39277ae000-7f39277bc000 r-xp 00000000 08:01 920644 7f39277bc000-7f39279bc000 ---p 0000e000 08:01 920644 7f39279bc000-7f39279bd000 rw-p 0000e000 08:01 920644 7f39279bd000-7f39279cb000 r-xp 00000000 08:01 920639 7f39279cb000-7f3927bca000 ---p 0000e000 08:01 920639 7f3927bca000-7f3927bcb000 rw-p 0000d000 08:01 920639 7f3927bcb000-7f3927bde000 r-xp 00000000 08:01 920616 7f3927bde000-7f3927dde000 ---p 00013000 08:01 920616 7f3927dde000-7f3927ddf000 rw-p 00013000 08:01 920616 7f3927ddf000-7f3927dee000 r-xp 00000000 08:01 920618 7f3927dee000-7f3927fed000 ---p 0000f000 08:01 920618 7f3927fed000-7f3927fee000 rw-p 0000e000 08:01 920618 7f3927fee000-7f3927ffe000 r-xp 00000000 08:01 920589 7f3927ffe000-7f39281fd000 ---p 00010000 08:01 920589 7f39281fd000-7f39281fe000 rw-p 0000f000 08:01 920589 7f39281fe000-7f392820c000 r-xp 00000000 08:01 920595 7f392820c000-7f392840b000 ---p 0000e000 08:01 920595 7f392840b000-7f392840c000 rw-p 0000d000 08:01 920595 7f392840c000-7f3928564000 r-xp 00000000 08:01 163881 7f3928564000-7f3928764000 ---p 00158000 08:01 163881 7f3928764000-7f3928767000 r--p 00158000 08:01 163881 7f3928767000-7f3928769000 rw-p 0015b000 08:01 163881 7f3928769000-7f392876e000 rw-p 7f3928769000 7f392876e000-7f392877b000 r-xp 00000000 08:01 163943 7f392877b000-7f392897b000 ---p 0000d000 08:01 163943 7f392897b000-7f392897c000 rw-p 0000d000 08:01 163943 7f392897c000-7f39289fc000 r-xp 00000000 08:01 163899 7f39289fc000-7f3928bfb000 ---p 00080000 08:01 163899 7f3928bfb000-7f3928bfd000 rw-p 0007f000 08:01 163899 7f3928bfd000-7f3928cec000 r-xp 00000000 08:01 67377 7f3928cec000-7f3928eec000 ---p 000ef000 08:01 67377 7f3928eec000-7f3928ef2000 r--p 000ef000 08:01 67377 7f3928ef2000-7f3928ef5000 rw-p 000f5000 08:01 67377 7f3928ef5000-7f3928f08000 rw-p 7f3928ef5000 7f3928f08000-7f3928f1e000 r-xp 00000000 08:01 67919 7f3928f1e000-7f392911e000 ---p 00016000 08:01 67919 7f392911e000-7f392911f000 rw-p 00016000 08:01 67919 7f392911f000-7f3929121000 r-xp 00000000 08:01 163893 7f3929121000-7f3929321000 ---p 00002000 08:01 163893 7f3929321000-7f3929323000 rw-p 00002000 08:01 163893 7f3929323000-7f392943c000 r-xp 00000000 08:01 69821 7f392943c000-7f392963b000 ---p 00119000 08:01 69821 7f392963b000-7f3929640000 rw-p 00118000 08:01 69821 7f3929640000-7f3929651000 rw-p 7f3929640000 7f3929651000-7f392966e000 r-xp 00000000 08:01 163860 7f392984b000-7f392984f000 rw-p 7f392984b000 7f392986b000-7f392986e000 rw-p 7f392986b000 7f392986e000-7f3929870000 rw-p 0001d000 08:01 163860 7fff49d1b000-7fff49d30000 rw-p 7ffffffea000 00:00 0 7fff49dfe000-7fff49e00000 r-xp 7fff49dfe000 00:00 0 ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 Abandon Open_babel_crash.xyz
corruption (out): 0x00000000006b6ff0 ***
an>
onnectTheDotsEv+0x59a)[0x7f39293978ea]
FFormat12ReadMoleculeEPNS_6OBBaseEPNS_12OBConversionE+0x560)[0x7f39265f77a0]
BMoleculeFormat18ReadChemObjectImplEPNS_12OBConversionEPNS_8OBFormatE+0x7ce)[0x7f392660281e]
BMoleculeFormat14ReadChemObjectEPNS_12OBConversionE+0x12)[0x7f39265f8042]
on7ConvertEv+0x90)[0x7f39293a6400]
on7ConvertEPSiPSo+0x1f7)[0x7f39293a7c17]
on11FullConvertERSt6vectorISsSaISsEERSsS4+0x124e)[0x7f39293aad6e]
842a1c4]
an>
/usr/bin/babel
/usr/bin/babel
[heap]
00:00 0
00:00 0
/usr/lib/openbabel/2.1/crkformat.so
/usr/lib/openbabel/2.1/crkformat.so
/usr/lib/openbabel/2.1/crkformat.so
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/usr/lib/openbabel/2.1/yasaraformat.so
/usr/lib/openbabel/2.1/yasaraformat.so
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/usr/lib/openbabel/2.1/CSRformat.so
/usr/lib/openbabel/2.1/pcmodelformat.so
/usr/lib/openbabel/2.1/pcmodelformat.so
/usr/lib/openbabel/2.1/pcmodelformat.so
/usr/lib/openbabel/2.1/cmlformat.so
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/usr/lib/openbabel/2.1/inchiformat.so
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/usr/lib/openbabel/2.1/featformat.so
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/usr/lib/openbabel/2.1/featformat.so
/usr/lib/openbabel/2.1/APIInterface.so
/usr/lib/openbabel/2.1/APIInterface.so
/usr/lib/openbabel/2.1/APIInterface.so
/usr/lib/openbabel/2.1/cansmilesformat.so
/usr/lib/openbabel/2.1/cansmilesformat.so
/usr/lib/openbabel/2.1/cansmilesformat.so
/usr/lib/openbabel/2.1/boxformat.so
/usr/lib/openbabel/2.1/boxformat.so
/usr/lib/openbabel/2.1/boxformat.so
/usr/lib/openbabel/2.1/mopacformat.so
/usr/lib/openbabel/2.1/mopacformat.so
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/usr/lib/openbabel/2.1/jaguarformat.so
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/usr/lib/openbabel/2.1/nwchemformat.so
/usr/lib/openbabel/2.1/nwchemformat.so
/usr/lib/openbabel/2.1/nwchemformat.so
/usr/lib/openbabel/2.1/povrayformat.so
/usr/lib/openbabel/2.1/povrayformat.so
/usr/lib/openbabel/2.1/povrayformat.so
/usr/lib/openbabel/2.1/copyformat.so
/usr/lib/openbabel/2.1/copyformat.so
/usr/lib/openbabel/2.1/copyformat.so
/usr/lib/openbabel/2.1/mpdformat.so
/usr/lib/openbabel/2.1/mpdformat.so
/usr/lib/openbabel/2.1/mpdformat.so
/usr/lib/openbabel/2.1/amberformat.so
/usr/lib/openbabel/2.1/amberformat.so
/usr/lib/openbabel/2.1/amberformat.so
/usr/lib/openbabel/2.1/thermoformat.so
/usr/lib/openbabel/2.1/thermoformat.so
/usr/lib/openbabel/2.1/thermoformat.so
/usr/lib/openbabel/2.1/pdbformat.so
/usr/lib/openbabel/2.1/pdbformat.so
/usr/lib/openbabel/2.1/pdbformat.so
/usr/lib/openbabel/2.1/mpqcformat.so
/usr/lib/openbabel/2.1/mpqcformat.so
/usr/lib/openbabel/2.1/mpqcformat.so
/usr/lib/openbabel/2.1/hinformat.so
/usr/lib/openbabel/2.1/hinformat.so
/usr/lib/openbabel/2.1/hinformat.so
/usr/lib/openbabel/2.1/fhformat.so
/usr/lib/openbabel/2.1/fhformat.so
/usr/lib/openbabel/2.1/fhformat.so
/usr/lib/openbabel/2.1/reportformat.so
/usr/lib/openbabel/2.1/reportformat.so
/usr/lib/openbabel/2.1/reportformat.so
/usr/lib/openbabel/2.1/fingerprintformat.so
/usr/lib/openbabel/2.1/fingerprintformat.so
/usr/lib/openbabel/2.1/fingerprintformat.so
/usr/lib/openbabel/2.1/mmodformat.so
/usr/lib/openbabel/2.1/mmodformat.so
/usr/lib/openbabel/2.1/mmodformat.so
/usr/lib/openbabel/2.1/mdlformat.so
/usr/lib/openbabel/2.1/mdlformat.so
/usr/lib/openbabel/2.1/mdlformat.so
/usr/lib/openbabel/2.1/alchemyformat.so
/usr/lib/openbabel/2.1/alchemyformat.so
/usr/lib/openbabel/2.1/alchemyformat.so
/usr/lib/openbabel/2.1/molreportformat.so
/usr/lib/openbabel/2.1/molreportformat.so
/usr/lib/openbabel/2.1/molreportformat.so
/usr/lib/openbabel/2.1/rxnformat.so
/usr/lib/openbabel/2.1/rxnformat.so
/usr/lib/openbabel/2.1/rxnformat.so
/usr/lib/openbabel/2.1/cacaoformat.so
/usr/lib/openbabel/2.1/cacaoformat.so
/usr/lib/openbabel/2.1/cacaoformat.so
/usr/lib/openbabel/2.1/gaussformat.so
/usr/lib/openbabel/2.1/gaussformat.so
/usr/lib/openbabel/2.1/gaussformat.so
/usr/lib/openbabel/2.1/qchemformat.so
/usr/lib/openbabel/2.1/qchemformat.so
/usr/lib/openbabel/2.1/qchemformat.so
/usr/lib/openbabel/2.1/pubchem.so
/usr/lib/openbabel/2.1/pubchem.so
/usr/lib/openbabel/2.1/pubchem.so
/usr/lib/openbabel/2.1/xmlformat.so
/usr/lib/openbabel/2.1/xmlformat.so
/usr/lib/openbabel/2.1/xmlformat.so
/usr/lib/openbabel/2.1/PQSformat.so
/usr/lib/openbabel/2.1/PQSformat.so
/usr/lib/openbabel/2.1/PQSformat.so
/usr/lib/openbabel/2.1/smilesformat.so
/usr/lib/openbabel/2.1/smilesformat.so
/usr/lib/openbabel/2.1/smilesformat.so
/usr/lib/openbabel/2.1/cacheformat.so
/usr/lib/openbabel/2.1/cacheformat.so
/usr/lib/openbabel/2.1/cacheformat.so
/usr/lib/openbabel/2.1/cssrformat.so
/usr/lib/openbabel/2.1/cssrformat.so
/usr/lib/openbabel/2.1/cssrformat.so
/usr/lib/openbabel/2.1/zindoformat.so
/usr/lib/openbabel/2.1/zindoformat.so
/usr/lib/openbabel/2.1/zindoformat.so
/usr/lib/openbabel/2.1/chemtoolformat.so
/usr/lib/openbabel/2.1/chemtoolformat.so
/usr/lib/openbabel/2.1/chemtoolformat.so
/usr/lib/openbabel/2.1/viewmolformat.so
/usr/lib/openbabel/2.1/viewmolformat.so
/usr/lib/openbabel/2.1/viewmolformat.so
/usr/lib/openbabel/2.1/chemdrawctformat.so
/usr/lib/openbabel/2.1/chemdrawctformat.so
/usr/lib/openbabel/2.1/chemdrawctformat.so
/usr/lib/openbabel/2.1/unichemformat.so
/usr/lib/openbabel/2.1/unichemformat.so
/usr/lib/openbabel/2.1/unichemformat.so
/usr/lib/openbabel/2.1/fastaformat.so
/usr/lib/openbabel/2.1/fastaformat.so
/usr/lib/openbabel/2.1/fastaformat.so
/usr/lib/openbabel/2.1/mol2format.so
/usr/lib/openbabel/2.1/mol2format.so
/usr/lib/openbabel/2.1/mol2format.so
/usr/lib/openbabel/2.1/xedformat.so
/usr/lib/openbabel/2.1/xedformat.so
/usr/lib/openbabel/2.1/xedformat.so
/usr/lib/openbabel/2.1/chemdrawcdxformat.so
/usr/lib/openbabel/2.1/chemdrawcdxformat.so
/usr/lib/openbabel/2.1/chemdrawcdxformat.so
/usr/lib/openbabel/2.1/cifformat.so
/usr/lib/openbabel/2.1/cifformat.so
/usr/lib/openbabel/2.1/cifformat.so
/usr/lib/openbabel/2.1/xyzformat.so
/usr/lib/openbabel/2.1/xyzformat.so
/usr/lib/openbabel/2.1/xyzformat.so
/usr/lib/openbabel/2.1/tinkerformat.so
/usr/lib/openbabel/2.1/tinkerformat.so
/usr/lib/openbabel/2.1/tinkerformat.so
/usr/lib/openbabel/2.1/fastsearchformat.so
/usr/lib/openbabel/2.1/fastsearchformat.so
/usr/lib/openbabel/2.1/fastsearchformat.so
/usr/lib/libxml2.so.2.6.31
/usr/lib/libxml2.so.2.6.31
/usr/lib/libxml2.so.2.6.31
00:00 0
/usr/lib/openbabel/2.1/cdxmlformat.so
/usr/lib/openbabel/2.1/cdxmlformat.so
/usr/lib/openbabel/2.1/cdxmlformat.so
/usr/lib/openbabel/2.1/fchkformat.so
/usr/lib/openbabel/2.1/fchkformat.so
/usr/lib/openbabel/2.1/fchkformat.so
/usr/lib/openbabel/2.1/freefracformat.so
/usr/lib/openbabel/2.1/freefracformat.so
/usr/lib/openbabel/2.1/freefracformat.so
/usr/lib/openbabel/2.1/turbomoleformat.so
/usr/lib/openbabel/2.1/turbomoleformat.so
/usr/lib/openbabel/2.1/turbomoleformat.so
/usr/lib/openbabel/2.1/shelxformat.so
/usr/lib/openbabel/2.1/shelxformat.so
/usr/lib/openbabel/2.1/shelxformat.so
/usr/lib/openbabel/2.1/gamessformat.so
/usr/lib/openbabel/2.1/gamessformat.so
/usr/lib/openbabel/2.1/gamessformat.so
/usr/lib/openbabel/2.1/ghemicalformat.so
/usr/lib/openbabel/2.1/ghemicalformat.so
/usr/lib/openbabel/2.1/ghemicalformat.so
/usr/lib/openbabel/2.1/bgfformat.so
/usr/lib/openbabel/2.1/bgfformat.so
/usr/lib/openbabel/2.1/bgfformat.so
/usr/lib/openbabel/2.1/cccformat.so
/usr/lib/openbabel/2.1/cccformat.so
/usr/lib/openbabel/2.1/cccformat.so
/lib/libc-2.7.so
/lib/libc-2.7.so
/lib/libc-2.7.so
/lib/libc-2.7.so
00:00 0
/lib/libgcc_s.so.1
/lib/libgcc_s.so.1
/lib/libgcc_s.so.1
/lib/libm-2.7.so
/lib/libm-2.7.so
/lib/libm-2.7.so
/usr/lib/libstdc++.so.6.0.9
/usr/lib/libstdc++.so.6.0.9
/usr/lib/libstdc++.so.6.0.9
/usr/lib/libstdc++.so.6.0.9
00:00 0
/usr/lib/libz.so.1.2.3.3
/usr/lib/libz.so.1.2.3.3
/usr/lib/libz.so.1.2.3.3
/lib/libdl-2.7.so
/lib/libdl-2.7.so
/lib/libdl-2.7.so
/usr/lib/libopenbabel.so.2.1.1
/usr/lib/libopenbabel.so.2.1.1
/usr/lib/libopenbabel.so.2.1.1
00:00 0
/lib/ld-2.7.so
00:00 0
00:00 0
/lib/ld-2.7.so
[stack]
[vdso]
[vsyscall]

Discussion

Nobody/Anonymous - 2010-01-05

Open_babel_crash.cif

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Vincent Favre-Nicolin - 2010-01-05

This seems to happen in ConnectTheDots, see below when running with --errorlevel 4, within valgrind. Kekulize is called 126 times, and EndModify complains about being called once too many..

Vincent

valgrind babel ---errorlevel 4 Open_babel_crash.cif Open_babel_crash.xyz

*** Open Babel Audit Log in ReadChemObjectImpl
OpenBabel::Read molecule Crystallographic Information File
==============================
Open Babel Audit Log in ConnectTheDots
Ran OpenBabel::ConnectTheDots
==============================
Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
==============================
Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
==============================
Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize

[SNIP: call to Kekulize a total number of 126 times]

==============================
Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
==============================
Open Babel Audit Log in AssignSpinMultiplicity
Ran OpenBabel::AssignSpinMultiplicity
==============================
Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
Open Babel Debugging Message in EndModify
_mod is negative - EndModify() called too many times
==============================
*** Open Babel Audit Log in WriteChemObjectImpl
OpenBabel::Write molecule XYZ cartesian coordinates format
1 molecule converted

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Geoff Hutchison - 2010-03-02

This definitely works with OB trunk (2.3). I'm going to mark this as "pending" further comment using the 2.3 snapshot.

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SourceForge Robot - 2010-03-18

This Tracker item was closed automatically by the system. It was
previously set to a Pending status, and the original submitter
did not respond within 14 days (the time period specified by
the administrator of this Tracker).

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crash when converting a CIF file

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#575 crash when converting a CIF file

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