[Debian-med-packaging] Bug#917143: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: COREDUMP

[Bernhard Übelacker]

Dear Maintainer,
just tried to get some more information out of the crash.

It was not showing up with t-coffee 12 compiled in testing.
Just with switching to unstable and recompiling t-coffee
the crash manifested when
building libbio-tools-run-alignment-tcoffee-perl-1.7.4.

Unfortunately the signal is 'eaten' and therefore no
core file is generated.
With a modification adding a call to gdb I was able to get one.

Below is the backtrace of the first failing pid.
Some more information is in the attached file describing how
the information was collected.

It looks like the static array name_list is accessed beyond the
initilialized memory.

Kind regards,
Bernhard


$ gdb -q -ex 'set pagination off' -ex 'set width 0' -ex 'directory /home/benutzer/source/t-coffee/try2/t-coffee-12.00.7fb08c2/t_coffee_source' /usr/bin/t_coffee --core ./core.3995
Reading symbols from /usr/bin/t_coffee...Reading symbols from /usr/lib/debug/.build-id/26/7314cbd87aae405b78889c1e3af85806aea901.debug...done.
done.
[New LWP 3995]
Core was generated by `/usr/bin/t_coffee'.
#0  0x00007fe6b33eb7f7 in __GI___waitpid (pid=4065, stat_loc=stat_loc at entry=0x7ffe74a7b488, options=options at entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
30      ../sysdeps/unix/sysv/linux/waitpid.c: Datei oder Verzeichnis nicht gefunden.
Source directories searched: /home/benutzer/source/t-coffee/try2/t-coffee-12.00.7fb08c2/t_coffee_source:$cdir:$cwd
(gdb) bt
#0  0x00007fe6b33eb7f7 in __GI___waitpid (pid=4065, stat_loc=stat_loc at entry=0x7ffe74a7b488, options=options at entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
#1  0x00007fe6b336980f in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149
#2  0x000055f262eef2b0 in error_exit (exit_code=11) at util_lib/util.c:10008
#3  <signal handler called>
#4  0x000055f262ebb84d in decode_name (name=name at entry=0x55f26537f1f0 "TCTAG_53775_4", mode=mode at entry=2) at util_lib/reformat.c:14644
#5  0x000055f262ebbbdd in translate_name (name=0x55f26537f1f0 "TCTAG_53775_4") at util_lib/reformat.c:14575
#6  0x000055f262ebd1da in get_fasta_sequence (fname=<optimized out>, comment_out=0x0) at util_lib/reformat.c:5304
#7  0x000055f262ebe7b7 in main_read_aln (name=name at entry=0x55f265366250 "/var/tmp/tco/tcoifo4u0ng3972//11383988396", A=0x55f26538bf90, A at entry=0x0) at util_lib/reformat.c:1532
#8  0x000055f262f28db1 in aln_file2constraint_list (alname=alname at entry=0x55f265366250 "/var/tmp/tco/tcoifo4u0ng3972//11383988396", CL=CL at entry=0x55f2652de520, weight_mode=weight_mode at entry=0x55f265363858 "sim") at util_lib/util_constraints_list.c:4304
#9  0x000055f262f3decf in read_constraint_list (CL=0x55f2652de520, in_fname=<optimized out>, in_mode=in_mode at entry=0x55f262f582fc "aln", mem_mode=mem_mode at entry=0x55f262f6702f "disk", weight_mode=weight_mode at entry=0x55f265363858 "sim") at util_lib/util_constraints_list.c:2368
#10 0x000055f262f3dfaa in retrieve_lib_job (job=0x55f2635cb990) at util_lib/util_constraints_list.c:473
#11 0x000055f262f20bb5 in fork_subset_produce_list (CL=CL at entry=0x55f2652de520, method=method at entry=0x55f263617d71 "clustalw_pair", job=0x55f2635cb990, job at entry=0x55f263ab2f00, nproc=<optimized out>, local_stderr=0x55f2634f9bd0, mem_mode=0x55f2634f9bd0 "\204,\255", <incomplete sequence \373>, weight=<optimized out>, S=0x55f263617d71) at util_lib/util_constraints_list.c:177
#12 0x000055f262f3d1bf in produce_list (CL=CL at entry=0x55f2652de520, S=<optimized out>, method=method at entry=0x55f263617d71 "clustalw_pair", weight=weight at entry=0x55f2639d4020 "default", mem_mode=mem_mode at entry=0x55f2635cfbc0 "mem") at util_lib/util_constraints_list.c:94
#13 0x000055f262f3dc70 in read_constraint_list (CL=CL at entry=0x55f2652de520, in_fname=<optimized out>, in_mode=in_mode at entry=0x0, mem_mode=mem_mode at entry=0x55f2635cfbc0 "mem", weight_mode=weight_mode at entry=0x55f2639d4020 "default") at util_lib/util_constraints_list.c:2332
#14 0x000055f262f3e253 in fork_read_n_constraint_list (fname=0x55f2636139e0, n_list=<optimized out>, in_mode=0x0, mem_mode=0x55f2635cfbc0 "mem", weight_mode=0x55f2639d4020 "default", type=<optimized out>, local_stderr=0x55f2634f9bd0, CL=0x55f2652de520, seq_source=0x55f2639a9560 "ANY", nproc=8) at util_lib/util_constraints_list.c:2218
#15 0x000055f262f3e812 in read_n_constraint_list (fname=0x55f2636139e0, n_list=4, in_mode=0x0, mem_mode=0x55f2635cfbc0 "mem", weight_mode=0x55f2639d4020 "default", type=0x55f2635c74a0 "", local_stderr=0x55f2634f9bd0, CL=0x55f2652de520, seq_source=0x55f2639a9560 "ANY") at util_lib/util_constraints_list.c:2141
#16 0x000055f262e697f0 in batch_main (argc=<optimized out>, argv=<optimized out>) at t_coffee_lib/t_coffee.c:4942
#17 0x000055f262d905ad in main (argc=<optimized out>, argv=<optimized out>) at t_coffee_lib/t_coffee.c:179


#4  0x000055f262ebb84d in decode_name (name=name at entry=0x55f26537f1f0 "TCTAG_53775_4", mode=mode at entry=2) at util_lib/reformat.c:14644
14644             return name_list[i-1][0];