#23 gap4 do not run

v1.5.3
closed-postponed
Gap4 (50)
5
2005-01-27
2005-01-11
Anonymous
No

I am not able to strart gap4 from new version (1-5-3).
This is message from gnome terminal:
honza@matiasovicj:~/gsoft/staden/staden-linux-1-5-3/linux-bin
$ ./gap4 invalid command name "load_alignment_matrix"
while executing
"load_alignment_matrix [keylget gap_defs
ALIGNMENT.MATRIX_FILE]"
(file
"/home/honza/gsoft/staden/staden-linux-1-5-3/linux-bin/../lib/gap/gap.tcl"
line 674)

Other apps from this version seems to work OK. Also
previous version (1.4.1) works well.
I am running Ubuntu Linux (warty) on P4, 512M Ram.
matiasovicj at vfu.cz

Discussion

  • Nobody/Anonymous

    Logged In: NO

    I have got the same errors, but when I changed the linux
    operation
    system, it will work !?!

    suse 8.2 -> gap4 worked
    suse 9.0 -> gap4 crash with tcl error
    suse 9.2 -> gap4 worked

    I used exactly the same staden source tree.

    I think, the only different library loaded is the libX11.so
    from OS that causes the crash.

    bsenf at imb-jena.de

     
  • Nobody/Anonymous

    Logged In: NO

    I have got the same errors, but when I changed the linux
    operation
    system, it will work !?!

    suse 8.2 -> gap4 worked
    suse 9.0 -> gap4 crash with tcl error
    suse 9.2 -> gap4 worked

    I used exactly the same staden source tree.

    I think, the only different library loaded is the libX11.so
    from OS that causes the crash.

    bsenf at imb-jena.de

     
  • Bastien Chevreux

    Logged In: YES
    user_id=98533

    Bug reproducible on a freshly installed system: SuSE 9.2 on
    an Xeon with AMD64 extensions (but OS is installed in 32 bit
    mode).

    - staden 1.5.3: bug as described originally
    - staden 1.4.3 and 2003.0b1 work

    Any idea what could cause this?

    Regards,
    Bastien

     
  • James Bonfield

    James Bonfield - 2005-01-19
    • assigned_to: nobody --> jkbonfield
     
  • James Bonfield

    James Bonfield - 2005-01-19

    Logged In: YES
    user_id=154581

    The usual way of working out the cause of such library
    conflicts is to set STADEN_DEBUG environment variable to 1.
    It's probably a missing gcc/g77 library - I should rebuild
    the distribution to include that (although most systems have
    it anyway).

    The load_alignment_matrix issue is simply a symptom of the
    libgap.so library failing to load correctly.
    Load_alignment_matrix is the first function called from it.

    Could you try setting STADEN_DEBUG and report the messages
    please.

    James

     
  • Nobody/Anonymous

    Logged In: NO

    Dear James. I try to set STADEN_DEBUG variable to 1, but
    with no effect. Here is message from terminal:
    honza@matiasovicj:$ echo $STADEN_DEBUG
    1
    honza@matiasovicj:~/gsoft/staden/staden-linux-1-5-3/linux-bin
    $ ./gap4
    invalid command name "load_alignment_matrix"
    while executing
    "load_alignment_matrix [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
    (file
    "/home/honza/gsoft/staden/staden-linux-1-5-3/linux-bin/../lib/gap/gap.tcl"
    line 674)

    Jan Matiasovic

     
  • Bastien Chevreux

    Logged In: YES
    user_id=98533

    I did. Output and method on how to resolve below:

    linux:/home/bach>gap4
    invalid command name "load_alignment_matrix"
    while executing
    "load_alignment_matrix [keylget gap_defs
    ALIGNMENT.MATRIX_FILE]"
    (file "/opt/biosw/staden/lib/gap/gap.tcl" line 674)
    linux:/home/bach>setenv STADEN_DEBUG 1
    linux:/home/bach>gap4
    load libcopy_reads.so => couldn't load file
    "libcopy_reads.so": libg2c.so.0: cannot open shared object
    file: No such file or directory
    load libcap2.so =>
    load libcap3.so =>
    load libfak2.so =>
    load libphrap.so =>
    load libgap.so => couldn't load file "libgap.so":
    libg2c.so.0: cannot open shared object file: No such file or
    directory
    invalid command name "load_alignment_matrix"
    while executing
    "load_alignment_matrix [keylget gap_defs
    ALIGNMENT.MATRIX_FILE]"
    (file "/opt/biosw/staden/lib/gap/gap.tcl" line 674)

    Sooooo ... libg2c.so.0 is the missing culprit. Now, how does
    one get it? If it is not to be found on your system, fetch
    the newest GCC compiler /http://gcc.gnu.org/) and compile it
    so that it installs itself in a location you have access to
    (e.g. "/home/YOURNAME/pub/local/"). Install it.

    Then add "/home/YOURNAME/pub/local/lib" to the
    LD_LIBRARY_PATH environment variable, better do it in the
    startup file.

    For me (using the tcsh as shell), the entry in the
    corresponding ~/.tcshrc looks like this:
    setenv LD_LIBRARY_PATH /home/bach/pub/linux/local/lib

    Take care for eventually predefined variables, adapt to your
    system!

    Regards,
    Bastien

     
  • James Bonfield

    James Bonfield - 2005-01-27

    Logged In: YES
    user_id=154581

    libg2c.so is part of gcc-g77-3.2.2-5.rpm on the system I
    used to build it (RedHat 9). I'll shortly be switching to
    Debian though so maybe things will be different next time!

    For the next release I'll probably build it using the
    C-conversion from the fortran code (there's not much fortran
    left) as this seems to work well under windows and requires
    no additional library support.

    As both the cause and solution are now known, I'm closing
    this bug. If you cannot find a g77 library package for your
    system please email me directly and I'll gladly send you the
    library binary.

    James

     
  • James Bonfield

    James Bonfield - 2005-01-27
    • status: open --> closed-postponed
     

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