Sorry, missed the file.
# buster amd64 qemu VM apt update apt dist-upgrade
apt install systemd-coredump fakeroot mc gdb htop dpkg-dev devscripts quilt apt build-dep libbio-tools-run-alignment-tcoffee-perl apt build-dep t-coffee wget http://ftp.de.debian.org/debian/pool/main/t/t-coffee/t-coffee_12.00.7fb08c2-1_amd64.deb dpkg -i t-coffee_12.00.7fb08c2-1_amd64.deb mkdir source/libbio-tools-run-alignment-tcoffee-perl/orig -p cd source/libbio-tools-run-alignment-tcoffee-perl/orig apt source libbio-tools-run-alignment-tcoffee-perl cd mkdir source/t-coffee/orig -p cd source/t-coffee/orig dget http://deb.debian.org/debian/pool/main/t/t-coffee/t-coffee_12.00.7fb08c2-1.dsc cd cd source/t-coffee cp orig try1 -a cd try1/t-coffee-12.00.7fb08c2 # add gdb call dpkg-buildpackage dpkg -i /home/benutzer/source/t-coffee/try1/t-coffee_12.00.7fb08c2-1_amd64.deb dpkg -i /home/benutzer/source/t-coffee/try1/t-coffee-dbgsym_12.00.7fb08c2-1_amd64.deb cd source/libbio-tools-run-alignment-tcoffee-perl cp orig try1 -a cd try1/libbio-tools-run-alignment-tcoffee-perl-1.7.4/ dpkg-buildpackage -b -> No crash ############## # switch to unstable apt update apt dist-upgrade cd source/t-coffee cp orig try2 -a cd try2/t-coffee-12.00.7fb08c2 cat <<EOF > debian/patches/0000-call-gdb-on-signal.patch Description: 0000-call-gdb-on-signal.patch Index: t-coffee-12.00.7fb08c2/t_coffee_source/util_lib/util.c =================================================================== --- t-coffee-12.00.7fb08c2.orig/t_coffee_source/util_lib/util.c +++ t-coffee-12.00.7fb08c2/t_coffee_source/util_lib/util.c @@ -10002,6 +10002,11 @@ void error_exit (int exit_code) { lock (getpid(), LERROR, LSET, "%d -- ERROR: COREDUMP: %s %s (%s)\n",getpid(), PROGRAM, VERSION, BUILD_INFO ); global_exit_signal=exit_code; + { + char buf[200]; + sprintf(buf, "gdb -q -n -batch -ex 'generate-core-file' -ex 'info thread' -ex 'info reg' -ex 'thread apply all bt full' -ex 'info share' -ex 'detach' -ex 'quit' --pid %d", getpid()); + system(buf); + } myexit (exit_code); } EOF echo 0000-call-gdb-on-signal.patch >> debian/patches/series dpkg-buildpackage dpkg -i /home/benutzer/source/t-coffee/try2/t-coffee_12.00.7fb08c2-1_amd64.deb dpkg -i /home/benutzer/source/t-coffee/try2/t-coffee-dbgsym_12.00.7fb08c2-1_amd64.deb cd source/libbio-tools-run-alignment-tcoffee-perl cp orig try2 -a cd try2/libbio-tools-run-alignment-tcoffee-perl-1.7.4/ dpkg-buildpackage -b $ find -iname "*core*" ./core.3995 ./core.3996 ./core.3994 ./core.4000 $ 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@entry=0x7ffe74a7b488, options=options@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@entry=0x7ffe74a7b488, options=options@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@entry=0x55f26537f1f0 "TCTAG_53775_4", mode=mode@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@entry=0x55f265366250 "/var/tmp/tco/tcoifo4u0ng3972//11383988396", A=0x55f26538bf90, A@entry=0x0) at util_lib/reformat.c:1532 #8 0x000055f262f28db1 in aln_file2constraint_list (alname=alname@entry=0x55f265366250 "/var/tmp/tco/tcoifo4u0ng3972//11383988396", CL=CL@entry=0x55f2652de520, weight_mode=weight_mode@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@entry=0x55f262f582fc "aln", mem_mode=mem_mode@entry=0x55f262f6702f "disk", weight_mode=weight_mode@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@entry=0x55f2652de520, method=method@entry=0x55f263617d71 "clustalw_pair", job=0x55f2635cb990, job@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@entry=0x55f2652de520, S=<optimized out>, method=method@entry=0x55f263617d71 "clustalw_pair", weight=weight@entry=0x55f2639d4020 "default", mem_mode=mem_mode@entry=0x55f2635cfbc0 "mem") at util_lib/util_constraints_list.c:94 #13 0x000055f262f3dc70 in read_constraint_list (CL=CL@entry=0x55f2652de520, in_fname=<optimized out>, in_mode=in_mode@entry=0x0, mem_mode=mem_mode@entry=0x55f2635cfbc0 "mem", weight_mode=weight_mode@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 (gdb) up #1 0x00007fe6b336980f in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149 149 ../sysdeps/posix/system.c: Datei oder Verzeichnis nicht gefunden. (gdb) #2 0x000055f262eef2b0 in error_exit (exit_code=11) at util_lib/util.c:10008 warning: Source file is more recent than executable. 10008 system(buf); (gdb) #3 <signal handler called> (gdb) #4 0x000055f262ebb84d in decode_name (name=name@entry=0x55f26537f1f0 "TCTAG_53775_4", mode=mode@entry=2) at util_lib/reformat.c:14644 14644 return name_list[i-1][0]; (gdb) list util_lib/reformat.c:14584,14700 14584 char *decode_name (char *name, int mode) 14585 { 14586 static char ***name_list; 14587 static int n; 14588 static char tag[100]; 14589 int a; 14590 14591 if (mode==CLEAN) 14592 { 14593 for (a=0; a<n; a++) 14594 { 14595 vfree (name_list[a][0]); 14596 vfree (name_list[a][1]); 14597 vfree (name_list[a]); 14598 } 14599 vfree (name_list); 14600 tag[0]='\0'; 14601 } 14602 14603 //spacial modes 14604 if ( mode == CODELIST) 14605 { 14606 char *file; 14607 file=vtmpnam (NULL); 14608 for (a=0; a< n; a++) 14609 printf_file(file, "a", "#CODE: %s <=> %s\n", name_list[a][0], name_list[a][1]); 14610 return file; 14611 } 14612 if (mode ==DECODE && name_list==NULL)return name; 14613 if ( name==NULL) return name; 14614 14615 14616 14617 if (!tag[0]) 14618 { 14619 vsrand (0); 14620 sprintf ( tag, "TCTAG_%d",rand ()%100000); 14621 } 14622 14623 if ( mode==CODE) 14624 { 14625 for (a=0; a< n; a++) 14626 if ( strm (name, name_list[a][0]))return name_list[a][1]; 14627 14628 name_list=(char***)realloc (name_list, sizeof (char**)*(n+1)); 14629 name_list[n]=(char**)vcalloc (2, sizeof (char*)); 14630 name_list[n][0]=(char*)vcalloc (strlen (name)+1, sizeof (char)); 14631 name_list[n][1]=(char*)vcalloc (100, sizeof (char)); 14632 sprintf ( name_list[n][0], "%s", name); 14633 sprintf ( name_list[n][1], "%s_%d", tag,n+1); 14634 return name_list[n++][1]; 14635 } 14636 else if ( mode ==DECODE) 14637 { 14638 char *p; 14639 int i; 14640 if ( !(p=after_strstr (name, tag)))return name; 14641 else 14642 { 14643 sscanf (p, "_%d", &i); 14644 return name_list[i-1][0]; <<<<<<<<<<< 14645 } 14646 } 14647 else 14648 { 14649 printf_exit (EXIT_FAILURE, stderr,"Unknown Mode for Decode_name [FATAL:%s]", PROGRAM); 14650 } 14651 return NULL; 14652 } (gdb) print i $8 = 4 (gdb) print mode $9 = 2 (gdb) print p $10 = <optimized out> (gdb) print name $11 = 0x55f26537f1f0 "TCTAG_53775_4" (gdb) print name_list $12 = (char ***) 0x55f2635d00e0 (gdb) print name_list[0] $13 = (char **) 0x55f26535a050 (gdb) print *name_list[0] $14 = 0x55f265359d50 "CATH_RAT" (gdb) print name_list[1] $15 = (char **) 0x55f26536a410 (gdb) print *name_list[1] $16 = 0x55f26536a290 "OW0UmFQ1YB" (gdb) print name_list[2] $17 = (char **) 0x55f265383220 (gdb) print *name_list[2] $18 = 0x55f2653705e0 "PAPA_CARPA" (gdb) print name_list[3] $19 = (char **) 0x381 (gdb) print *name_list[3] Cannot access memory at address 0x381 (gdb) disassemble 0x000055f262ebb84d-0x30,0x000055f262ebb84d+0x20 Dump of assembler code from 0x55f262ebb81d to 0x55f262ebb86d: 0x000055f262ebb81d <decode_name(char*, int)+125>: (bad) 0x000055f262ebb81e <decode_name(char*, int)+126>: imul $0xc0854800,(%rdx),%eax 0x000055f262ebb824 <decode_name(char*, int)+132>: je 0x55f262ebb850 <decode_name(char*, int)+176> 0x000055f262ebb826 <decode_name(char*, int)+134>: lea 0x4(%rsp),%rdx 0x000055f262ebb82b <decode_name(char*, int)+139>: mov %rax,%rdi 0x000055f262ebb82e <decode_name(char*, int)+142>: lea 0xab7df(%rip),%rsi # 0x55f262f67014 0x000055f262ebb835 <decode_name(char*, int)+149>: xor %eax,%eax 0x000055f262ebb837 <decode_name(char*, int)+151>: callq 0x55f262d8f280 <sscanf@plt> 0x000055f262ebb83c <decode_name(char*, int)+156>: movslq 0x4(%rsp),%rdx 0x000055f262ebb841 <decode_name(char*, int)+161>: mov 0x172cc0(%rip),%rax # 0x55f26302e508 <_ZZ11decode_namePciE9name_list> 0x000055f262ebb848 <decode_name(char*, int)+168>: mov -0x8(%rax,%rdx,8),%rax => 0x000055f262ebb84d <decode_name(char*, int)+173>: mov (%rax),%r13 0x000055f262ebb850 <decode_name(char*, int)+176>: mov 0x8(%rsp),%rcx 0x000055f262ebb855 <decode_name(char*, int)+181>: xor %fs:0x28,%rcx 0x000055f262ebb85e <decode_name(char*, int)+190>: mov %r13,%rax 0x000055f262ebb861 <decode_name(char*, int)+193>: jne 0x55f262ebbb38 <decode_name(char*, int)+920> 0x000055f262ebb867 <decode_name(char*, int)+199>: add $0x18,%rsp 0x000055f262ebb86b <decode_name(char*, int)+203>: pop %rbx 0x000055f262ebb86c <decode_name(char*, int)+204>: pop %rbp End of assembler dump. (gdb) print/x $rax $21 = 0x381
