Gap4 error

2005-10-25
2013-04-18
  • Hi,

    gap4 in the most recent version (staden-linux-1-6-0/linux-bin/gap4)
    produces an error while starting up:

    linux-bin]$ invalid command name "load_alignment_matrix"
        while executing
    "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
        (file ".../staden-linux-1-6-0/linux-bin/../lib/gap/gap.tcl" line 683).

    Any fix/enlightenment is greatly appreciated.
    Edith

     
    • James Bonfield
      James Bonfield
      2005-10-27

      This typically happens when one of the libraries has failed to load; specifically libgap.so in this case.

      Set the STADEN_DEBUG environment variable and run again to see what library it is complaining about. It's possible that I forgot to include something in the linux distribution (it's happened time enough before!), but it's maybe also simply that there's a dependency on some system library that's not installed. There's so much variation under linux it can be hard to spot all these.

      As a hunch, I'd say you miss the libg2c.so file.

      James

       
    • Indeed, libg2c.so was missing. But after installing it,
      I still get a  "couldn't load file" message:

      $ load libcopy_reads.so =>
      load libitcl3.3.so =>
      load libitk3.3.so =>
      load libiwidgets.so => couldn't load file "libiwidgets.so": libiwidgets.so: cannot open shared object file: No such file or directory
      load libcap2.so =>
      load libcap3.so =>
      load libfak2.so =>
      load libphrap.so =>
      load libhaplo.so =>
      load libgap.so =>

      thanks for your help,
      Edith

       
    • James Bonfield
      James Bonfield
      2005-11-16

      This is harmless. Gap4 will whinge about any "load_package" command that doesn't have an associated compiled binary library, despite the fact that in some cases such a library legitimately does not exist. Fortunately it only complains when the STADEN_DEBUG variable is set as normally it harmlessly glosses over such things.

      Is Gap4 starting up and working for you?

       
    • Hi,

      I've got that with STADEN_DEBUG enabled:
      load libcopy_reads.so =>
      load libitcl3.3.so =>
      load libitk3.3.so =>
      load libiwidgets.so => couldn't load file "libiwidgets.so": libiwidgets.so: cannot open shared object file: No such file or directory
      load libcap2.so =>
      load libcap3.so =>
      load libfak2.so =>
      load libphrap.so =>
      load libhaplo.so =>
      load libgap.so =>

      I know now it is not a problem.

      My problem is:
      When i try to browse on my Redhat Linux AS, Xeon 64 bit quad cpu, it's working fine until i get through a NFS mounted drive with a SUN Solaris OS.  I can't see the folder structure or any . or .. folder name.  I know it is not a security problem or access problem.

      Do you have an idea about that ?

      Thanks for your help.

       
    • Hi James,

      yes Gap4 is working ok. And without STADEN_DEBUG
      variable set, no error messages are obtained.

      thanks a lot,
      Edith

       
    • I'm absolute beginner with Fedora4. What I'm doing wrong? I think I did get libg2c.so installed as adviced, how can i verify?Error is still there:

      $ set STADEN_DEBUG
      $ ./gap4
      invalid command name "load_alignment_matrix"
          while executing
      "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
          (file "/staden-linux-1-5-3/linux-bin/../lib/gap/gap.tcl" line 674)

      And spin just hangs, does not load.
      Please help
      Morian

       
    • If i try version 1-6-0, the error is on  line 683 as above...
      Morian

       
    • after strace ./gap4 >
      and proper install of lib2c.so and libstdc++5 gap4 works fine.
      Morian

       
    • hi i am working on fedora core 5 and gap4 ahs this error
      gap4
      invalid command name "load_alignment_matrix"
          while executing
      "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
          (file "/opt/staden-linux/lib/gap/gap.tcl" line 683)

      i had to do a lot of config file hacking to get pregap and spin working because the scripts mess with teh $MACHINE.

       
    • At the enda I have solved this problem but I have lost too much time with it.
      This is an information to mandirva 2007 users:
      libg2c.so library cames with the fortrand 77 compiler. You can install it with this command:
      urpmi gcc3.3-g77

      PD.
      In my opinion developers must be more carefull with this "common instalation problems" and include their solution in de documentation, or better, make installation packages ".rpm" or ".deb".
      J. ALEjandrO

       
    • James Bonfield
      James Bonfield
      2007-04-20

      Agreed I've been slacking rather a lot of late with regards to such things, but it's also a time issue. "The developers" is me only, part time on this :/. The big problem though is hundreds of linux distributions. A lot may happen to use .rpm or .deb packages but that doesn't really help much as listing the packages they depend on will vary enormously from system to system. Some have libg2c.so in one package name, so put it in another, etc. How do you know which one to list the dependency for?

      About all we can do here is to list the usual suspects along with what to look for when trying to resolve them. The alternative is a somewhat clumsy (but widely used to avoid just this hell) approach of statically linking everything.

      In reality what needs fixing more than anything else is the Makefile system and ease of compilation. If it was tidied up to all be using autoconf then all it needs is a few people to build on each flavour of linux (although I shudder at using libtool again for the dynamic libraries as that programs a total abomination and was the cause of a lack of portability in early io_libs).

      James

       
    • I am having the same problem.
      I am using Suse 10.2 and libg2c.so is absent.
      Where can I get this library?
      Thanks
      Denis

       
    • I've just fixed this problem on SUSE 10.1. The missing rpm for me was compat-g77-3.3.5-17.x86_64.rpm. You may need an i386 version for your hardware or a more recent version for 10.2 SUSE. This rpm was not on the OpenSUSE 10.1 CDs but I found it via RPMbone.
      Good Luck
      Paul

       
    • Thanks Paul.
      I installed compat-g77 and solved the gap4 problem. However, I found that I have another problem. spin does not load. I just hangs there doing nothing and I don't get any error messages to guide me.
      Any suggestion?
      Thanks,
      Denis

       
    • hi i,m new to linux, was trying to install 1-6-0 but only pregap4 seems to work, while running gap4 i always get an error message
      invalid command name "load_alignment_matrix"
          while executing "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
          (file "/home/guest/Desktop/staden-linux-1-6-0/linux-bin/../lib/gap/gap.tcl" line 683)
      can anyone help....

       
    • Try installing compat-77. This is what fixed the problem for me and others.
      Good luck
      Denis

       
    • Hi Im a peruvian student and also have the same problem, im using UBUNTU, i got this msg when run debug mode

      load libcopy_reads.so => couldn't load file "libcopy_reads.so": /usr/local/staden-linux-1-6-0/linux-bin/../lib/linux-binaries/libstdc++.so.5: version `GLIBCPP_3.2' not found (required by /usr/local/staden-linux-1-6-0/linux-bin/../lib/linux-binaries/libmutlib.so)
      load libitcl3.3.so =>
      load libitk3.3.so =>
      load libiwidgets.so => couldn't load file "libiwidgets.so": libiwidgets.so: cannot open shared object file: No such file or directory
      load libcap2.so =>
      load libcap3.so =>
      load libfak2.so =>
      load libphrap.so =>
      load libhaplo.so => couldn't load file "libhaplo.so": /usr/local/staden-linux-1-6-0/linux-bin/../lib/linux-binaries/libstdc++.so.5: version `GLIBCPP_3.2' not found (required by /usr/local/staden-linux-1-6-0/linux-bin/../lib/linux-binaries/libmutlib.so)
      load libgap.so => couldn't load file "libgap.so": /usr/local/staden-linux-1-6-0/linux-bin/../lib/linux-binaries/libstdc++.so.5: version `GLIBCPP_3.2' not found (required by /usr/local/staden-linux-1-6-0/linux-bin/../lib/linux-binaries/libmutlib.so)
      invalid command name "load_alignment_matrix"
          while executing
      "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
          (file "/usr/local/staden-linux-1-6-0/linux-bin/../lib/gap/gap.tcl" line 683)

      I think i tried to replace libstdc++.so.5 making "ln command" with the new version 6.0.9 as suggested another forum, and "GLIBCPP_3.2" warning comes out, now im more confused than i first started, can somebody help me?!

       
    • on Fedora 10 only final error occurs but gap4 is not working, the rest of  packages do

      invalid command name "load_alignment_matrix"
      while executing
      "load_alignment_matrix [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
      (file "/usr/local/staden-linux-1-7-0/linux-bin/../lib/gap/gap.tcl" line 683)

      compat-gcc-34-g77 is installed (equivalent to compat-g77 on Fedora 10) and sym links to libraries
      libstdc++.so.5
      lib2c.so
      are set... in /urs/lib

       
    • on Fedora 10 one needs
      libstdc++.so.5.0.7 toghether with the link libstdc++.so.5 to it

      and link to libstdc++.so.6.0.10 wouldn't work

      the right library comes with
      compat-libstdc++-33.i386 : Compatibility standard C++ libraries

      libstdc++.so.6.0.10 is in
      compat-libstdc++-296.i386 : Compatibility 2.96-RH standard C++ libraries

       
  • hi i m shahid and  want to install staden on ubunto 9 but when i run make commad it give error like this
    collect2: ld returned 1 exit status
    make: ***  Error 1
    make: Leaving directory `/home/ebiokit/Downloads/staden-2.0.0b4-src/prefinish'
    make: ***  Error 2
    can any body help me about this error.thanks in advance.

     
  • I assume your compilation is with the latest  2.0.0b4 source tree?

    I need more than the final few lines you listed here, although my guess is a missing symbol, perhaps due to missing a library? Ideally these should all be spotted at configure time though.

    James