[phylocom-user] *** buffer overflow detected ***: ./phylocom terminated

Cam Webb cwebb at oeb.harvard.edu
Sun Apr 29 16:53:24 PDT 2012


Hi Simon,

   $ ./phylocom bladj output.tree.new

is not a valid command.  If both `phylo' and `ages' exist in the current 
directory, then

   $ ./phylocom bladj > output.tree.new

is valid, and will write to output.tree.new

Best,

Cam


On Fri, 27 Apr 2012, Simon Queenborough wrote:

> Hi,
>
> I am using ubuntu 11.04, and just installed phylocom, which worked ok.
> However, when I try and run any command in phylocom, it aborts as
> follows below.
>
> I am not au fait enough with linux to know what is going on, and any
> help would be much appreciated!
>
> Thanks, Simon
>
> simon at simon-desktop-office:~/phylocom/phylocom-4.2/src$ ./phylocom bladj
> output.tree.new
> *** buffer overflow detected ***: ./phylocom terminated
> ======= Backtrace: =========
> /lib/i386-linux-gnu/libc.so.6(__fortify_fail+0x45)[0xb7692c75]
> /lib/i386-linux-gnu/libc.so.6(+0xe7a77)[0xb7691a77]
> /lib/i386-linux-gnu/libc.so.6(+0xe6edf)[0xb7690edf]
> ./phylocom[0x804d73f]
> ./phylocom[0x804bba6]
> ./phylocom[0x8049444]
> /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0xb75c3113]
> ./phylocom[0x8048b71]
> ======= Memory map: ========
> 08048000-08070000 r-xp 00000000 08:01 2097828
> /home/simon/phylocom/phylocom-4.2/src/phylocom
> 08070000-08071000 r--p 00027000 08:01 2097828
> /home/simon/phylocom/phylocom-4.2/src/phylocom
> 08071000-08072000 rw-p 00028000 08:01 2097828
> /home/simon/phylocom/phylocom-4.2/src/phylocom
> 08072000-0807e000 rw-p 00000000 00:00 0
> 08eda000-08efb000 rw-p 00000000 00:00 0          [heap]
> b758a000-b75a6000 r-xp 00000000 08:01 28967866
> /lib/i386-linux-gnu/libgcc_s.so.1
> b75a6000-b75a7000 r--p 0001b000 08:01 28967866
> /lib/i386-linux-gnu/libgcc_s.so.1
> b75a7000-b75a8000 rw-p 0001c000 08:01 28967866
> /lib/i386-linux-gnu/libgcc_s.so.1
> b75a8000-b75aa000 rw-p 00000000 00:00 0
> b75aa000-b7722000 r-xp 00000000 08:01 28971568
> /lib/i386-linux-gnu/libc-2.13.so
> b7722000-b7724000 r--p 00178000 08:01 28971568
> /lib/i386-linux-gnu/libc-2.13.so
> b7724000-b7725000 rw-p 0017a000 08:01 28971568
> /lib/i386-linux-gnu/libc-2.13.so
> b7725000-b7728000 rw-p 00000000 00:00 0
> b7728000-b7750000 r-xp 00000000 08:01 28971572
> /lib/i386-linux-gnu/libm-2.13.so
> b7750000-b7751000 r--p 00028000 08:01 28971572
> /lib/i386-linux-gnu/libm-2.13.so
> b7751000-b7752000 rw-p 00029000 08:01 28971572
> /lib/i386-linux-gnu/libm-2.13.so
> b7763000-b7765000 rw-p 00000000 00:00 0
> b7765000-b7766000 r-xp 00000000 00:00 0          [vdso]
> b7766000-b7784000 r-xp 00000000 08:01 28967972
> /lib/i386-linux-gnu/ld-2.13.so
> b7784000-b7785000 r--p 0001d000 08:01 28967972
> /lib/i386-linux-gnu/ld-2.13.so
> b7785000-b7786000 rw-p 0001e000 08:01 28967972
> /lib/i386-linux-gnu/ld-2.13.so
> bf85c000-bf87d000 rw-p 00000000 00:00 0          [stack]
> Aborted
>
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