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#694 closed defect (fixed)

ARB crashes when importing a RAxML EPA tree

Reported by:	guest	Owned by:	westram
Priority:	normal	Milestone:
Component:	Import / Export	Version:
Keywords:		Cc:	jgerken@…

Description

Affected ARB versions: probably all. Tested with arb-6.0.1.rev12565, carb-devel-6.1.rev14693

Steps to reproduce:

open SILVA 123 SSU Ref NR 99 in ARB (https://www.arb-silva.de/fileadmin/silva_databases/release_123/ARB_files/SSURef_NR99_123_SILVA_12_07_15_opt.arb.tgz)
import the attached
ARB crashes

Console output:

Error: 'Internal buffer overflow (size=64000, used=64002)
'
Can't continue - terminating..

-------------------- ARB-backtrace 'GBK_terminate (reason above) ':
/bioinf/software/arb/ubuntu-10.04/arb-trunk-14435/lib/libCORE.so(GBK_dump_backtrace(_IO_FILE*, char const*)+0x34)[0x7f537fb2dde4]
/bioinf/software/arb/ubuntu-10.04/arb-trunk-14435/lib/libCORE.so(GBK_terminate(char const*)+0x49)[0x7f537fb2e039]
/bioinf/software/arb/ubuntu-10.04/arb-trunk-14435/lib/libCORE.so(+0x110f5)[0x7f537fb2e0f5]
/bioinf/software/arb/ubuntu-10.04/arb-trunk-14435/lib/libCORE.so(+0x112fc)[0x7f537fb2e2fc]
/bioinf/software/arb/ubuntu-10.04/arb-trunk-14435/lib/libCORE.so(GBS_vglobal_string_copy(char const*, __va_list_tag*)+0x1b)[0x7f537fb2e69b]
/bioinf/software/arb/ubuntu-10.04/arb-trunk-14435/lib/libCORE.so(GBS_global_string_copy(char const*, ...)+0x8d)[0x7f537fb2e89d]
arb_ntree(TreeReader::add_warningf(char const*, ...)+0xba)[0x597e5a]
arb_ntree(TreeReader::setBranchName_acceptingBootstrap(TreeNode*, char*&)+0xcc)[0x596cfc]
arb_ntree(TreeReader::eat_and_set_name_and_length(TreeNode*, float&)+0x14e)[0x5975de]
arb_ntree(TreeReader::load_named_node(float&)+0xce)[0x59795e]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x1b3)[0x597813]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
arb_ntree(TreeReader::load_named_node(float&)+0x8d)[0x59791d]
arb_ntree(TreeReader::load_subtree(float&)+0x33)[0x597693]
-------------------- End of backtrace

Change History (3)

comment:1 Changed 9 years ago by guest

Unfortunately, I cannot add an attachment here. Please request it per mail.

comment:2 Changed 9 years ago by westram

Owner changed from devel to westram
Status changed from new to _started

Buffer overflow caused by too many warnings

comment:3 Changed 9 years ago by westram

Resolution set to fixed
Status changed from _started to closed

by [14697]

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