#250 gatekeeper -F option triggers segfault

gatekeeper
pending-fixed
Brian Walenz
None
5
2014-02-18
2013-07-31
eernst
No

gatekeeper -o ./asm.gkpStore.BUILDING -T ./j4.cor.clean.test.frg

works, but

gatekeeper -o ./asm.gkpStore.BUILDING -T -F ./j4.cor.clean.test.frg

gives:

[0] gatekeeper::AS_UTL_catchCrash(int, siginfo, void) + 0x27 [0x4229f7]
[1] /lib64/libpthread.so.0::(null) + 0xf500 [0x2ac44bac1500]
[2] gatekeeper::AS_GKP_reportError(int, unsigned int, ...) + 0x123 [0x4198e3]
[3] gatekeeper::checkLibraryDistances(LibraryMesg, int) + 0x1e5 [0x40a2b5]
[4] gatekeeper::Check_LibraryMesg(LibraryMesg
, int, unsigned int) + 0x15b [0x40a5bb]
[5] gatekeeper::(null) + 0x9b8 [0x408138]
[6] /lib64/libc.so.6::(null) + 0xfd [0x2ac44bcedcdd]
[7] gatekeeper() [0x405cd9]

j4.cor.clean.test.frg:

{VER
ver:2
}
{LIB
act:A
acc:j4
ori:I
mea:5290
std:473
src:
.
nft:1
fea:
doNotOverlapTrim=1
.
}
{FRG
act:A
acc:j40
rnd:1
sta:G
lib:j4
pla:0
loc:0
src:
.
seq:
AAGTGCGTAGTGTGTGCATGCTTGTGTCCGTACGTGTGTGCGAAAGTGTAAACGTTCGTGGGCGTGTACATGCGTGCGTACTTGTGTGCGAAATTGTGTAC
.
qlt:
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
.
hps:
.
clr:0,101
}
{FRG
act:A
acc:j41
rnd:1
sta:G
lib:j4
pla:0
loc:0
src:
.
seq:
GGAGGAGCCGAGGGACATCGACGACGACGCCTTCGGGGTAATCGGGTTAGTAGTGCGTAATCTTCGCAATCCTTACCCTATAGATTAGATTAGATTAGACG
.
qlt:
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
.
hps:
.
clr:0,101
}

Discussion

  • Brian Walenz
    Brian Walenz
    2013-08-01

    Thanks. It was an error in new error reporting code in gatekeeper. Fixed and committed to svn 4366.

     
  • Brian Walenz
    Brian Walenz
    2013-08-01

    • status: open --> pending-fixed
    • assigned_to: Brian Walenz