Problem compiling Staden Package 2.0.0b4

2010-03-18
2013-04-18
  • Hi everyone,

    I am trying to install the Staden Package on a Ubuntu 9.10, architecture i386. When I type ./configure -with-tclconfig=/opt/ActiveTcl-8.5/lib/ -with-tkconfig=/opt/ActiveTcl-8.5/lib/ -with-samtools=/opt/samtools-0.1.7_x86_64-linux/, everything works great, except for,

    External packages used:
    curl:      via /usr/local/bin/curl-config
    zlib:      DIR (system)
    liblzma:   DIR
    samtools:  ***NOT FOUND***
    io_lib:    via /usr/local/bin/io_lib-config
    Tcl:       via /opt/ActiveTcl-8.5/lib/tclConfig.sh
    Tk:        via /opt/ActiveTcl-8.5/lib/tkConfig.sh
    tklib:     /usr/share/tcltk/tklib0.5
    Iwidgets:  /usr/share/tcltk/iwidgets4.0.1
    Itcl:      /usr/share/tcltk/itcl3.2
    Itk:       /usr/share/tcltk/itk3.2

    Then, I tried make, and the result was,

    sheet.c:1119: error: ‘Sheet’ has no member named ‘yflip’
    sheet.c:1119: error: ‘Sheet’ has no member named ‘rows’
    sheet.c:1119: error: ‘Sheet’ has no member named ‘border_width’
    sheet.c:1119: error: ‘Sheet’ has no member named ‘border_width’
    make: ***  Error 1
    make: Leaving directory `/home/andre/Downloads/staden-2.0.0b4-src/tk_utils'
    make: ***  Error 2

     
  • André Bertran
    André Bertran
    2010-03-18

    Can anyone help me with this?

    Thanks,

    André

     
  • James Bonfield
    James Bonfield
    2010-03-19

    This is rather odd, but I assume it's somehow including the wrong header file - perhaps finding another sheet.h installed somewhere. It's not a problem I've seen before.

    When compiling sheet.c you should see a command line looking something like:

    gcc -g -O2  -I/include -I/nfs/users/nfs_j/jkb/sys/x86_64/include -I/include -DUSE_NON_CONST  -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../tk_utils -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../Misc -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../tk_utils -I/software/badger/include -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../seq_utils   -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q  -fPIC   -o sheet.o -c /nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../tk_utils/sheet.c

    It won't be precisely that as it depends where you're building it and what -with options you used, but just before those errors you will see the command line it attempted to use.

    If you cd to the tk_utils subdirectory and cut and paste that line again, then you should get the same results; it starts compialtion and then fails with the errors you see.  If you then replace the "-o sheet.o" section with "-E" instead you'll see the code it's actually attempting to compile, along with the locaton of the header files it included, etc. This will help me a lot in trying to diagnose the problem. You'll probably also want to redirect it using "> filename". Eg if I edited the command line I saw above I'd get:

    gcc -E -g -O2  -I/include -I/nfs/users/nfs_j/jkb/sys/x86_64/include -I/include -DUSE_NON_CONST  -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../tk_utils -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../Misc -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../tk_utils -I/software/badger/include -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../seq_utils   -I/nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q  -fPIC   -E -c /nfs/users/nfs_j/jkb/staden/trunk/src/build.seq1q/../tk_utils/sheet.c > out

    Sorry that's a bit cryptic, but I can't really see how else I can debug this given that it works fine here. Could you please try this and email me the results? (jkb at sanger or via sourceforge).

    James