Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • BmoreHawk
    Junior Member
    • May 2013
    • 2
    #1

    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 ?
    Tags: installation, samtools, solaris11
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    Have you tried appending the LD_LIBRARY_PATH variable with paths for ncurses and zlib?

    Comment

    • swbarnes2
      Senior Member
      • May 2008
      • 910
      #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

      • sridhar28
        Member
        • May 2013
        • 15
        #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

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142
          #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

          • sridhar28
            Member
            • May 2013
            • 15
            #6
            Hi geno,

            Thank you for the reply.

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

            Thanks
            Sridhar

            Comment

            • GenoMax
              Senior Member
              • Feb 2008
              • 7142
              #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:

              zlib Home Site
              http://zlib.net/


              Index of /pub/gnu/ncurses
              http://ftp.gnu.org/pub/gnu/ncurses/


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

              Comment

              • sridhar28
                Member
                • May 2013
                • 15
                #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

                Previous template Next

                Latest Articles

                Collapse
                • SEQadmin2
                  Nine Things a Sample Prep Scientist Thinks About Before Sequencing
                  by SEQadmin2


                  I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

                  Here are nine questions we think about, in roughly the order they matter, before...
                  Yesterday, 07:11 AM
                • SEQadmin2
                  From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
                  by SEQadmin2


                  Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

                  The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
                  ...
                  06-02-2026, 10:05 AM
                • SEQadmin2
                  Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends
                  by SEQadmin2


                  With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.

                  Introduction

                  Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
                  05-22-2026, 06:42 AM
                View All

                ad_right_rmr

                Collapse

                News

                Collapse
                Topics Statistics Last Post
                Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2
                Started by SEQadmin2, 06-17-2026, 06:09 AM
                0 responses
                20 views
                0 reactions
                		 Last Post SEQadmin2
                by SEQadmin2
                06-17-2026, 06:09 AM  
                Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2
                Started by SEQadmin2, 06-09-2026, 11:58 AM
                0 responses
                38 views
                0 reactions
                		 Last Post SEQadmin2
                by SEQadmin2
                06-09-2026, 11:58 AM  
                A New Method Makes Hantavirus Genome Analysis Faster and More Accessible by SEQadmin2
                Started by SEQadmin2, 06-05-2026, 10:09 AM
                0 responses
                44 views
                0 reactions
                		 Last Post SEQadmin2
                by SEQadmin2
                06-05-2026, 10:09 AM  
                A New Single-Cell Method Maps DNA-Protein Interactions by SEQadmin2
                Started by SEQadmin2, 06-04-2026, 08:59 AM
                0 responses
                49 views
                0 reactions
                		 Last Post SEQadmin2
                by SEQadmin2
                06-04-2026, 08:59 AM  
                View All
                Working...