Problem compiling Staden Package 2.0.0b4

  • Nobody/Anonymous

    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/
    Tk:        via /opt/ActiveTcl-8.5/lib/
    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?



  • 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).



Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:

No, thanks