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Install Staden-src-1-7-0 on /linux-x86_64

  • Nobody/Anonymous

    Hi, I have problem compile the package and here are what I have done:

    # first compile all the libraries
    cd /usr/local/staden/staden-src-1-7-0
    export STADENROOT=`pwd`
    . staden.profile
    cd src
    make -f Makefile.thirdparty

    # the program ran for a while then an error appear saying /usr/local/staden/staden-src-1-7-0/lib/iwidgets can't be removed because it's a directory. So I manually delete the directory and rerun make:

    rm /usr/local/staden/staden-src-1-7-0/lib/iwidgets
    make -f Makefile.rhirdparty

    # at this point everything seems to be fine (but I was just guessing)
    # Then I compile the staden package
    cd /usr/local/staden/staden-src-1-7-0
    make 2>&1 | tee make.out

    # then the program ran for a while and show the errors below (far below):

    In file included from include/Read.h:43,
                     from sff/linux-x86_64-binaries/../sff.c:26:
    include/os.h:131:1: warning: "NEED_VA_COPY" redefined
    <command line>:10:1: warning: this is the location of the previous definition
    cc -L../lib/linux-x86_64-binaries  -shared -o ../lib/linux-x86_64-binaries/  read/linux-x86_64-binarie
    s/Read.o read/linux-x86_64-binaries/translate.o read/linux-x86_64-binaries/scf_extras.o utils/linux-x86_64-binar
    ies/find.o utils/linux-x86_64-binaries/mach-io.o utils/linux-x86_64-binaries/traceType.o utils/linux-x86_64-bina
    ries/read_alloc.o utils/linux-x86_64-binaries/compress.o utils/linux-x86_64-binaries/open_trace_file.o utils/lin
    ux-x86_64-binaries/hash_table.o utils/linux-x86_64-binaries/mFILE.o utils/linux-x86_64-binaries/vlen.o scf/linux
    -x86_64-binaries/read_scf.o scf/linux-x86_64-binaries/write_scf.o scf/linux-x86_64-binaries/misc_scf.o exp_file/
    linux-x86_64-binaries/expFileIO.o plain/linux-x86_64-binaries/seqIOPlain.o abi/linux-x86_64-binaries/fpoint.o ab
    i/linux-x86_64-binaries/seqIOABI.o alf/linux-x86_64-binaries/seqIOALF.o ctf/linux-x86_64-binaries/ctfCompress.o
    ctf/linux-x86_64-binaries/seqIOCTF.o ztr/linux-x86_64-binaries/compression.o ztr/linux-x86_64-binaries/ztr_trans
    late.o ztr/linux-x86_64-binaries/ztr.o sff/linux-x86_64-binaries/sff.o  -lz   -lmisc  -L/usr/lib64 -lcurl -L/usr
    /kerberos/lib -L/usr/kerberos/lib64 -lssl -lcrypto -lgssapi_krb5 -lkrb5 -lcom_err -lk5crypto -lresolv -ldl -lz -
    lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lresolv -L/usr/kerberos/lib -L/usr/kerberos/lib64 -lidn -lssl -lcrypto
    -lssl -lcrypto -lgssapi_krb5 -lkrb5 -lcom_err -lk5crypto -lresolv -ldl -lz -lz
    /usr/bin/ld: ../lib/linux-x86_64-binaries/libz.a(crc32.o): relocation R_X86_64_32 against `a local symbol' can n
    ot be used when making a shared object; recompile with -fPIC
    ../lib/linux-x86_64-binaries/libz.a: could not read symbols: Bad value
    collect2: ld returned 1 exit status
    make[2]: *** [../lib/linux-x86_64-binaries/] Error 1
    make[2]: Leaving directory `/usr/local/staden/staden-src-1-7-0/src/io_lib'
    make[1]: *** [io_lib] Error 2
    make[1]: Leaving directory `/usr/local/staden/staden-src-1-7-0/src'
    make: *** [all] Error 2

    # I am going to send you an email with an attachment of 'make.out' file in addition to the above same text. Is the email address '' working?? Do you mind sending your reply to also? THank you very much!

    • Nobody/Anonymous

      I got the exact same problem on my x86_64 system. Did you solve yours?

    • Nobody/Anonymous

      Hallo Jean,

      ... I solved the problem you had using the following procedure:

      The problem is indeed the compiled libz.a . To recompile that piece using the -fPIC compiler option solves the problem. How to do this:

      1. go into the directory <wherever_you_inst_it>/src/zlib (zlib should be a symlink to zlib-1.2.2)
      2. do a "make clean"
      3. edit Makefile and change the following line




      4. run "make" - it should compile the zlib.a file
      5. cp the zlib.a file to ../lib/linux-x86_64-binaries/libz.a
      6. cd to <wherever_you_inst_it>/src and do a "make -f Makefile.thirdparty" again

      ... I encounter in another problem after that:

      the wrong(32bit) libX was uses in linking stuff in tk_utils. To prevent that problem you will have to edit the <wherever_you_inst_it>/src/mk/ file.

      Change the line:

      XBIN    = /usr/X11R6/lib


      XBIN    = /usr/X11R6/lib64 (or wherever X11 is installed)

      This was on my RHEL Linux - but should be the same on Fedora for instance ...

      Doing again a "make -f Makefile.thirdparty" should now compile the rest of the Staden package ...

      ... hope this will help you a bit ... I posted it also to the list ...



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