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the problem of compiling source guide in ubuntu 10.10

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Old   July 23, 2011, 22:52
Default the problem of compiling source guide in ubuntu 10.10
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bojiezhang
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hello every member :
I have a probelm when compiling source guide using ubuntu 10.10.I have already installed doxygen,graphviz, texlive-latex-base and qt4-dev-tools, but it show errors as follow:
*** buffer overflow detected ***: doxygen terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x50)[0xb756c970]
/lib/libc.so.6(+0xe486a)[0xb756b86a]
/lib/libc.so.6(+0xe3fa8)[0xb756afa8]
/lib/libc.so.6(_IO_default_xsputn+0x9e)[0xb74f1a2e]
/lib/libc.so.6(_IO_vfprintf+0x115)[0xb74c4325]
/lib/libc.so.6(__vsprintf_chk+0xad)[0xb756b05d]
doxygen[0x819e5f2]
doxygen[0x819ea83]
doxygen[0x804dd03]
doxygen[0x806c0b9]
doxygen[0x806e8ce]
doxygen[0x806ea38]
doxygen[0x806ea6c]
doxygen[0x806ea6c]
doxygen[0x806ea6c]
doxygen[0xec]
doxygen[0x804a20f]
/lib/libc.so.6(__libc_start_main+0xe7)[0xb749dce7]
doxygen[0x804a141]
======= Memory map: ========
0-084b9000 r-xp 08:05 /usr/bin/doxygen
084b9000-084ba000 r--p 08:05 /usr/bin/doxygen
084ba000-084c6000 rw-p 08:05 /usr/bin/doxygen
084c6000-0 rw-p 00:00 0
0a-135d5000 rw-p 00:00 0 [heap]
b6a-b6a rw-p 00:00 0
b6a-b6cc9000 rw-p 00:00 0
b6e0b000-b6f4d000 rw-p 00:00 0
b6f8d000-b rw-p 00:00 0
b-b r--p 08:05 /usr/lib/locale/locale-archive
b-b rw-p 00:00 0
b-b75de000 r-xp 08:05 /lib/libc-2.12.1.so
b75de000-b75e0000 r--p 08:05 /lib/libc-2.12.1.so
b75e0000-b75e1000 rw-p 08:05 /lib/libc-2.12.1.so
b75e1000-b75e4000 rw-p 00:00 0
b75e4000-b75fe000 r-xp 08:05 /lib/libgcc_s.so.1
b75fe000-b75ff000 r--p 08:05 /lib/libgcc_s.so.1
b75ff000-b rw-p 0001a000 08:05 /lib/libgcc_s.so.1
b-b r-xp 08:05 /lib/libm-2.12.1.so
b-b r--p 08:05 /lib/libm-2.12.1.so
b-b rw-p 08:05 /lib/libm-2.12.1.so
b-b r-xp 08:05 /usr/lib/libstdc++.so.6.0.14
b-b r--p 000de000 08:05 /usr/lib/libstdc++.so.6.0.14
b-b770a000 rw-p 000e2000 08:05 /usr/lib/libstdc++.so.6.0.14
b770a000-b rw-p 00:00 0
b-b r-xp 08:05 /lib/libpthread-2.12.1.so
b-b ---p 08:05 /lib/libpthread-2.12.1.so
b-b r--p 08:05 /lib/libpthread-2.12.1.so
b-b rw-p 08:05 /lib/libpthread-2.12.1.so
b-b772c000 rw-p 00:00 0
b773e000-b rw-p 00:00 0
b-b r-xp 00:00 0 [vdso]
b-b775d000 r-xp 08:05 /lib/ld-2.12.1.so
b775d000-b775e000 r--p 0001b000 08:05 /lib/ld-2.12.1.so
b775e000-b775f000 rw-p 0001c000 08:05 /lib/ld-2.12.1.so
bf8e0000-bf rw-p 00:00 0 [stack]
Aborted
+ chmod -R a+rX html latex man
+ echo
+ echo Done doxygen
Done doxygen
+ echo

I can not solve it ,please help me ! Thank you in advance !
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Old   July 24, 2011, 06:36
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Bruno Santos
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Greetings bojiezhang,

That is one strange crash that doxygen made.

OK, here's a few more things we'll need to know to try and help you:
  1. How much RAM does your machine have?
  2. Which architecture of Ubuntu did you install? You can check by running:
    Code:
    uname -m
    If it outputs x86_64, then it's the 64bit version.
  3. For which OpenFOAM version and package are you trying to build the code documentation? Is it OpenFOAM 2.0.0, 2.0.x, 1.7.1 or 1.7.x? And are you building it from source or did you install the .deb packages for Ubuntu?
  4. If you installed the .deb packages of OpenFOAM, are you building the code documentation as root? If so, did you also source the etc/bashrc file while in root mode?
Best regards,
Bruno
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Old   July 24, 2011, 11:03
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bojiezhang
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Thank you for you reply, the next part is the detail information:
1.RAM
:~$ free
total used free shared buffers cached
Mem: 4051456 753464 3297992 0 60552 314272

2.architecture of Ubuntu
:~$ uname -m
i686

3.I install OpenFOAM 2.0.0, and use the OpenFOAM-2.0.0.gtgz and the ThirdParty-2.0.0.gtgz to install.

4.I build the code documentation as user(not root) and I also source the etc/bashrc file.

Thank you very much!
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Old   July 24, 2011, 17:02
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Bruno Santos
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Hi bojiezhang,

This is one crazy bug... well, I got the same crash with an identical installation in a virtual machine (Ubuntu 10.10 i686 with 4GB of RAM). Here's how I managed to fix the problem:
  1. Downloaded the previous version of Doxygen that will install in Ubuntu 10.10 without any problems; such version is available here: https://launchpad.net/ubuntu/maveric...oxygen/1.6.3-1
    Download the package "doxygen_1.6.3-1_i386.deb (1.6 MiB)".
  2. In a terminal, go to the folder where doxygen_1.6.3-1_i386.deb is and run:
    Code:
    sudo dpkg -i doxygen_1.6.3-1_i386.deb
And then build the code documentation for OpenFOAM once again! It took me almost an hour to build the whole documentation.


If instead you prefer to step up to a more recent version of Doxygen, here's what you can do (keep in mind that this could break your installation ):
  1. Edit the file "/etc/apt/sources.list". One way of doing this is by running:
    Code:
    gksu gedit /etc/apt/sources.list
    It will ask for super user permissions.
  2. Then find the lines that have something like this:
    Code:
    deb http://pt.archive.ubuntu.com/ubuntu/ maverick main restricted
    deb-src http://pt.archive.ubuntu.com/ubuntu/ maverick main restricted
    Copy those two lines you have got.
  3. Go to the end of the file and paste those two lines.
  4. Now change on the new lines from maverick to natty; e.g.:
    Code:
    deb http://pt.archive.ubuntu.com/ubuntu/ natty main restricted
    deb-src http://pt.archive.ubuntu.com/ubuntu/ natty main restricted
  5. Now run:
    Code:
    sudo apt-get update
    sudo apt-get install doxgen
    These should upgrade Doxygen up to 1.7.3; Ubuntu 10.10 has Doxygen 1.7.1, so this is a nice upgrade
  6. When you're done, edit "/etc/apt/sources.list" again and comment or remove those two lines you added. Save and close.
  7. Clear up the package list by running:
    Code:
    sudo apt-get update
And there you have it: an upgraded Doxygen version.
The steps I've written down should only involve the packages that Doxygen really needs, so It shouldn't damage the Ubuntu installation you've got. The last two steps are for clearing up the package list, so there won't be any more unwanted updates, or so I hope.

Good luck!
Bruno
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Old   July 25, 2011, 01:41
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bojiezhang
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Dear Bruno :
I use "doxygen_1.6.3-1_i386.deb" and have solved it ! Thank you very much !
bojiezhang
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