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  • samtools compiling issues on Solaris 11

    Hi all,

    I'm quite new to the field and I'm having issues compiling samtools 0.1.19 from source. I'm using a SunOs Solaris 11 platform and this is the message displayed ....
    (I have installed zlib 1.2.3 and GNU ncurses 5.9 as indicated in the INSTALL file)...

    am2bcf_indel.c: In function ‘bcf_call_gap_prep’:
    bam2bcf_indel.c:408:3: warning: implicit declaration of function ‘alloca’
    gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
    bam_tview_curses.c:7:2: warning: #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
    In file included from bam_tview.h:11:0,
    from bam_tview_curses.c:19:
    faidx.h:76:50: error: expected ‘;’, ‘,’ or ‘)’ before ‘register’
    bam_tview_curses.c:287:2: warning: #warning "No curses library is available; tview with curses is disabled."
    *** Error code 1
    make: Fatal error: Command failed for target `bam_tview_curses.o'
    Current working directory /home/username/samtools/samtools-0.1.19
    *** Error code 1
    The following command caused the error:
    target=`echo all-recur | sed s/-recur//`; \
    wdir=`pwd`; \
    list='. bcftools misc'; for subdir in $list; do \
    cd $subdir; \
    make CC="gcc" DFLAGS="-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1" CFLAGS="-g -Wall -O2" \
    INCLUDES="-I." LIBPATH="" $target || exit 1; \
    cd $wdir; \
    done;
    make: Fatal error: Command failed for target `all-recur'


    I tried to make clean and modify the Makefile as follows

    `-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
    comment out the line starting with `LIBCURSES='. as suggested in the INSTALL file

    but I still get an error...

    does anyone have an idea on what is going wrong ?

  • #2
    Have you tried appending the LD_LIBRARY_PATH variable with paths for ncurses and zlib?

    Comment


    • #3
      Random suggestion; at the suggestion of another informatics guy at my work, I altered the samtools Makefile so that it read


      Code:
      LIBCURSES=	-lncurses
      And that made it work for me. So maybe a small tweak to that line of the Makefile will fix your problem.

      Comment


      • #4
        Hi,
        I face same problem as mentioned. i am installing samtools version0.19 .
        The Error i am getting is
        warning: #warning "No curses library is available; tview with curses is disabled."
        gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview_html.c -o bam_tview_html.o
        gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lncurses -lm -lz -lpthread
        phase.o: In function `loadpos':
        /illumina/data/galaxy/apps/samtools/phase.c:475: undefined reference to `gzopen64'
        bedcov.o: In function `main_bedcov':
        /illumina/data/galaxy/apps/samtools/bedcov.c:69: undefined reference to `gzopen64'
        libbam.a(bam_import.o): In function `__bam_get_lines':
        /illumina/data/galaxy/apps/samtools/bam_import.c:76: undefined reference to `gzopen64'
        libbam.a(bam_import.o): In function `sam_open':
        /illumina/data/galaxy/apps/samtools/bam_import.c:472: undefined reference to `gzopen64'
        libbam.a(bam_import.o): In function `sam_header_read2':
        /illumina/data/galaxy/apps/samtools/bam_import.c:126: undefined reference to `gzopen64'
        libbam.a(bedidx.o):/illumina/data/galaxy/apps/samtools/bedidx.c:107: more undefined references to `gzopen64' follow
        collect2: ld returned 1 exit status
        make[1]: *** [samtools] Error 1
        make[1]: Leaving directory `/illumina/data/galaxy/apps/samtools'
        make: *** [all-recur] Error 1

        Even i tried to change "LIBCURSES= -lncurses" and try make. but again i am getting same error

        please suggest..

        Thanks
        Sridhar

        Comment


        • #5
          Originally posted by sridhar28 View Post
          Hi,
          I face same problem as mentioned. i am installing samtools version0.19 .
          The Error i am getting is
          warning: #warning "No curses library is available; tview with curses is disabled."
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview_html.c -o bam_tview_html.o
          gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lncurses -lm -lz -lpthread
          phase.o: In function `loadpos':
          /illumina/data/galaxy/apps/samtools/phase.c:475: undefined reference to `gzopen64'
          bedcov.o: In function `main_bedcov':
          /illumina/data/galaxy/apps/samtools/bedcov.c:69: undefined reference to `gzopen64'
          libbam.a(bam_import.o): In function `__bam_get_lines':
          /illumina/data/galaxy/apps/samtools/bam_import.c:76: undefined reference to `gzopen64'
          libbam.a(bam_import.o): In function `sam_open':
          /illumina/data/galaxy/apps/samtools/bam_import.c:472: undefined reference to `gzopen64'
          libbam.a(bam_import.o): In function `sam_header_read2':
          /illumina/data/galaxy/apps/samtools/bam_import.c:126: undefined reference to `gzopen64'
          libbam.a(bedidx.o):/illumina/data/galaxy/apps/samtools/bedidx.c:107: more undefined references to `gzopen64' follow
          collect2: ld returned 1 exit status
          make[1]: *** [samtools] Error 1
          make[1]: Leaving directory `/illumina/data/galaxy/apps/samtools'
          make: *** [all-recur] Error 1

          Even i tried to change "LIBCURSES= -lncurses" and try make. but again i am getting same error

          please suggest..

          Thanks
          Sridhar
          Have you installed the Zlib and NCURSES libraries?

          Comment


          • #6
            Hi geno,

            Thank you for the reply.

            I dint install those library.. could you please tell how to install it??

            Thanks
            Sridhar

            Comment


            • #7
              Originally posted by sridhar28 View Post
              Hi geno,

              Thank you for the reply.

              I dint install those library.. could you please tell how to install it??

              Thanks
              Sridhar
              I am rusty on solaris so there may be other ways to get this:





              Sunfreeware site: http://www.sunfreeware.com/source-list.html

              Comment


              • #8
                Hi Geno,

                Thanks for the links..

                i am using redhat linux system..
                after installing again i am facing same errors.. any thoughts??

                samtools binary will be created only after installing the libraries??
                Last edited by sridhar28; 05-30-2013, 09:29 PM.

                Comment

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