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  • NicolaLosito
    replied
    On an Ubuntu box all you will need is:

    Code:
    sudo apt-get install libncurses5 libncurses5-dev
    to solve the missing curses.h file not found error

    Leave a comment:


  • kausikmhg
    replied
    do yum install ncurses-devel , i hpe it will solve th issue

    recommended for Centos , RHEL

    Same problem faced and solved
    Kausik Bhattacharyya
    Delhi University

    Leave a comment:


  • dakl
    replied
    Not sure this is the appropriate thread for this problem.

    Anyhow, it looks like you're missing zlib. Did you try installing zlib-devel. If you're on RedHat/Fedora/CentOS, try

    sudo yum install zlib-devel

    //D

    Leave a comment:


  • ngadewal
    replied
    I am getting following error while installing samtools
    The update version of zlib and ncurses are installed.
    I tried to look posts but cold not find answer to "bgzf error"

    *********************************************************************************
    make[1]: Entering directory `/root/samtools-0.1.18'
    make[2]: Entering directory `/root/samtools-0.1.18'
    gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
    In file included from bgzf.c:36:
    bgzf.h:29:18: error: zlib.h: No such file or directory
    bgzf.c: In function ‘open_write’:
    bgzf.c:186: error: ‘Z_DEFAULT_COMPRESSION’ undeclared (first use in this function)
    bgzf.c:186: error: (Each undeclared identifier is reported only once
    bgzf.c:186: error: for each function it appears in.)
    bgzf.c: In function ‘deflate_block’:
    bgzf.c:297: error: ‘z_stream’ undeclared (first use in this function)
    bgzf.c:297: error: expected ‘;’ before ‘zs’
    bgzf.c:298: error: ‘zs’ undeclared (first use in this function)
    bgzf.c:305: warning: implicit declaration of function ‘deflateInit2’
    bgzf.c:305: error: ‘Z_DEFLATED’ undeclared (first use in this function)
    bgzf.c:306: error: ‘Z_DEFAULT_STRATEGY’ undeclared (first use in this function)
    bgzf.c:307: error: ‘Z_OK’ undeclared (first use in this function)
    bgzf.c:311: warning: implicit declaration of function ‘deflate’
    bgzf.c:311: error: ‘Z_FINISH’ undeclared (first use in this function)
    bgzf.c:312: error: ‘Z_STREAM_END’ undeclared (first use in this function)
    bgzf.c:313: warning: implicit declaration of function ‘deflateEnd’
    bgzf.c:345: warning: implicit declaration of function ‘crc32’
    bgzf.c: In function ‘inflate_block’:
    bgzf.c:371: error: ‘z_stream’ undeclared (first use in this function)
    bgzf.c:371: error: expected ‘;’ before ‘zs’
    bgzf.c:373: error: ‘zs’ undeclared (first use in this function)
    bgzf.c:380: warning: implicit declaration of function ‘inflateInit2’
    bgzf.c:381: error: ‘Z_OK’ undeclared (first use in this function)
    bgzf.c:385: warning: implicit declaration of function ‘inflate’
    bgzf.c:385: error: ‘Z_FINISH’ undeclared (first use in this function)
    bgzf.c:386: error: ‘Z_STREAM_END’ undeclared (first use in this function)
    bgzf.c:387: warning: implicit declaration of function ‘inflateEnd’
    bgzf.c: In function ‘check_header’:
    bgzf.c:405: error: ‘Z_DEFLATED’ undeclared (first use in this function)
    make[2]: *** [bgzf.o] Error 1
    make[2]: Leaving directory `/root/samtools-0.1.18'
    make[1]: *** [lib-recur] Error 1
    make[1]: Leaving directory `/root/samtools-0.1.18'
    make: *** [all-recur] Error 1
    *****************************************************************************

    Please help
    -Nikhil

    Leave a comment:


  • dakl
    replied
    I had to install ncurses-devel to make this work. I also changed the Makefile as suggested above.

    cheers
    Daniel

    Leave a comment:


  • satoshi936
    replied
    thank you, RockChalkJayhawk. I had a same problem and your answer solved the problem.

    Open SUSE 11.3
    samtools 0.1.18
    =======================================
    $ pwd
    /opt/utillities/samtools/samtools-0.1.18
    $ vi Makefile
    - change a line in "Makefile" as follows
    -------------------------------------------------
    original: LIBCURSES= -lcurses # -lXCurses
    changed: LIBCURSES= -lncurses # -lXCurses
    --------------------------------------------------
    $ make
    - compile worked well
    ========================================

    Leave a comment:


  • chaz81
    replied
    Thanks RCJ, just found your post and had been struggling with that!

    Leave a comment:


  • RockChalkJayhawk
    replied
    Problem Solved

    I ran into this problem as well. To get around it, change the makefile from
    Code:
    LIBCURSES= -lcurses
    to

    Code:
    LIBCURSES= -lncurses
    That should fix the problem.

    Leave a comment:


  • RockChalkJayhawk
    replied
    Originally posted by xinwu View Post
    Hi all,
    When I install SAMTool 0.1.8 on linux, I got error: cannot find -lcurses
    collect2: ld returned 1 exit status
    But I have libncurses.so installed under /usr/lib.
    After run rpm -qa | grep ncurses, I got:
    ncurses-devel-5.5-18.11
    ncurses-5.5-18.11
    yast2-ncurses-2.13.68-0.3
    ncurses-devel-32bit-5.5-18.11
    ncurses-32bit-5.5-18.11
    It seemed I've installed dependencies.
    Did I miss something? Thanks.
    Did you get this problem fixed?

    Leave a comment:


  • xinwu
    started a topic SAMTool install error about curses

    SAMTool install error about curses

    Hi all,
    When I install SAMTool 0.1.8 on linux, I got error: cannot find -lcurses
    collect2: ld returned 1 exit status
    But I have libncurses.so installed under /usr/lib.
    After run rpm -qa | grep ncurses, I got:
    ncurses-devel-5.5-18.11
    ncurses-5.5-18.11
    yast2-ncurses-2.13.68-0.3
    ncurses-devel-32bit-5.5-18.11
    ncurses-32bit-5.5-18.11
    It seemed I've installed dependencies.
    Did I miss something? Thanks.

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