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mmetta
2010-07-30
2013-04-18
  • mmetta
    mmetta
    2010-07-30

    hellow,
    i don't have much unix background. my computer have ubuntu installed. can you suggest me how i can install the package?

    thanks

     
  • mmetta
    mmetta
    2010-07-30

    i started to compile somehow. i get the following error when i type make.

    locks.o array_arith.o parse_db.o dstring.o     -lm
    gcc: usleep.o: No such file or directory
    gcc: error.o: No such file or directory
    gcc: xalloc.o: No such file or directory
    gcc: array.o: No such file or directory
    gcc: locks.o: No such file or directory
    gcc: dstring.o: No such file or directory
    make: ***  Error 1
    make: Leaving directory `/home/murali/Desktop/staden-2.0.0b7-src/build.myhost/Misc'
    make: ***  Error 2

    can you help me to resolve the issue.

    thanks

     
  • Hello,

    You haven't really given me enough information to work on.

    Which version of Ubuntu are you working on?

    Are you running on a 32 or 64 bit machine?

    Have you gone through the steps in the README.build file?

    What configure options did you use?

    Which directory were you in when you ran make?

    regards,

    Andrew

     
  • mmetta
    mmetta
    2010-07-30

    Ubuntu version: Ubuntu 10.04.1 LTS
    64 bit machine
    yes. i have gone through the steps and did as follows:
    cd  staden-2.0.0b7-src
    mkdir build.myhost
    cd build.myhost
    ../configure
    end of my out put at this stage is (if necessary i can paste entire thing):
    checking itcl directory… vers=/3004000/
    yes (/usr/share/tcltk/itcl3.4)
    checking itk directory… yes (/usr/share/tcltk/itk3.3)
    configure: creating ./config.status
    ../configure: line 15408: ./config.status: Permission denied
    ../configure: line 15421: ./config.status: Permission denied
    ../configure: line 15716: ./config.status: Permission denied
    ../configure: line 15723: ./config.status: Permission denied
    ../configure: line 15749: ./config.status: Permission denied
    ../configure: line 15763: ./config.status: Permission denied
    ../configure: line 15829: ./config.status: Permission denied
    ../configure: line 15838: ./config.status: Permission denied
    ../configure: line 15849: ./config.status: Permission denied
    ../configure: line 15852: ./config.status: Permission denied
    ../configure: line 16039: ./config.status: Permission denied
    ../configure: line 16051: ./config.status: Permission denied
    ../configure: line 16053: ./config.status: Permission denied
    ../configure: line 16136: ./config.status: Permission denied
    ../configure: line 16148: ./config.status: Permission denied
    ../configure: line 16150: ./config.status: Permission denied
    ../configure: line 16172: ./config.status: Permission denied
    ../configure: line 16344: ./config.status: Permission denied
    ../configure: line 16364: ./config.status: Permission denied
    ../configure: line 16378: ./config.status: Permission denied
    ../configure: line 16382: ./config.status: Permission denied
    ../configure: line 16472: ./config.status: Permission denied
    ../configure: line 16480: ./config.status: Permission denied
    ../configure: line 16482: ./config.status: Permission denied
    ../configure: line 16491: ./config.status: Permission denied
    ../configure: line 16492: ./config.status: Permission denied
    chmod: changing permissions of `./config.status': Operation not permitted
    config.status: creating Makefile
    config.status: creating system.mk
    config.status: creating shlib.conf
    config.status: creating staden_config.h
    config.status: staden_config.h is unchanged


    External packages used:
    curl:      via /usr/local/bin/curl-config
    zlib:      DIR (system)
    ncurses:   DIR (system)
    liblzma:   DIR
    samtools:  ***NOT FOUND***
    io_lib:    via /usr/bin/io_lib-config
    Tcl:       via /usr/lib/tclConfig.sh
    Tk:        via /usr/lib/tkConfig.sh
    tklib:     /usr/share/tcltk/tklib0.5
    Iwidgets:  /usr/share/tcltk/iwidgets4.0.1
    Itcl:      /usr/share/tcltk/itcl3.4
    Itk:       /usr/share/tcltk/itk3.3


    then i type "make".

    i get the error.

    I didn't use any configure options. do i have to use some options here?

    i am in build.myhost directory when i am running make.

    thanks a lot for your response.

    best regards
    m

     
  • The "permission denied" messages on config.status are odd.  Is there something unusual about the  permissions on the myhost.build directory?

    I didn't use any configure options. do i have to use some options here?/quote]

    You should need to if everything is in the default places.

    Could you do a "make clean" followed by a "make" and post the entire make output?  It might give me a better idea into what is going on.

    Andrew

     
  • mmetta
    mmetta
    2010-07-30

    i have installed samtools but i don't know why it still says cannot find.

     
  • mmetta
    mmetta
    2010-07-30

    here is the output after doing a "make clean" followed by "make"

    murali@murali-laptop:~/Desktop/staden-2.0.0b7-src/build.myhost$ make
    cd Misc && make -f /home/murali/Desktop/staden-2.0.0b7-src/build.myhost/../Misc/Makefile   BUILD=/home/murali/Desktop/staden-2.0.0b7-src/build.myhost SRC=/home/murali/Desktop/staden-2.0.0b7-src/build.myhost/../Misc SUBDIR=Misc all
    make: Entering directory `/home/murali/Desktop/staden-2.0.0b7-src/build.myhost/Misc'
    gcc -shared -g -O2  -I/include -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/murali/Desktop/staden-2.0.0b7-src/build.myhost/../Misc  -I/home/murali/Desktop/staden-2.0.0b7-src/build.myhost  -fPIC   -g -O2  -I/include -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/murali/Desktop/staden-2.0.0b7-src/build.myhost/../Misc  -I/home/murali/Desktop/staden-2.0.0b7-src/build.myhost  -fPIC  -L/home/murali/Desktop/staden-2.0.0b7-src/build.myhost/lib  -L/lib -Wl,-export-dynamic  -o /home/murali/Desktop/staden-2.0.0b7-src/build.myhost/lib/libmisc.so  crash.o date.o filenames.o files.o find.o shell.o strings.o usleep.o error.o xerror.o xalloc.o vlen.o FtoC.o getfile.o bitmap.o array.o locks.o array_arith.o parse_db.o dstring.o     -lm
    gcc: usleep.o: No such file or directory
    gcc: error.o: No such file or directory
    gcc: xalloc.o: No such file or directory
    gcc: array.o: No such file or directory
    gcc: locks.o: No such file or directory
    gcc: dstring.o: No such file or directory
    make: ***  Error 1
    make: Leaving directory `/home/murali/Desktop/staden-2.0.0b7-src/build.myhost/Misc'
    make: ***  Error 2

    thanks
    m

     
  • It looks like it is skipping the compilation stage and going straight on to the linking.

    My first thought is that the configuration has failed.  The fact that it could not write to the config.status file inside your build.myhost directory is suspicious.

    Try and delete everything in the build.myhost directory and run configure again (with samtools option set if you want to include it).  If that doesn't work email the config.log file to me at-  aw7 at sanger ac uk