Hi Shana, Are you really trying to compile version 0.1.1? Why not try 1.1 instead: https://sourceforge.net/projects/samtools/files/samtools/1.1/
Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Laboratory for Molecular and Cellular Cognition German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn Germany <devon.r...@dzne.de> On Thu, Nov 6, 2014 at 8:15 PM, Shana Burrowes <shana.burro...@gmail.com> wrote: > I am trying to install Samtools and I keep getting the error below. What > can I do to fix it?: > > ./libbam.a(bam_import.o): In function `ks_getuntil': > /home/stine/samtools-0.1.1/bam_import.c:12: undefined reference to `gzread' > ./libbam.a(bam_import.o): In function `bam_load_pos': > /home/stine/samtools-0.1.1/bam_import.c:51: undefined reference to > `gzdopen' > ./libbam.a(bam_import.o): In function `ks_getc': > /home/stine/samtools-0.1.1/bam_import.c:12: undefined reference to `gzread' > ./libbam.a(bam_import.o): In function `bam_load_pos': > /home/stine/samtools-0.1.1/bam_import.c:51: undefined reference to > `gzopen64' > ./libbam.a(bam_import.o): In function `sam_header_read2': > /home/stine/samtools-0.1.1/bam_import.c:103: undefined reference to > `gzdopen' > ./libbam.a(bam_import.o): In function `ks_getc': > /home/stine/samtools-0.1.1/bam_import.c:12: undefined reference to `gzread' > ./libbam.a(bam_import.o): In function `sam_header_read2': > /home/stine/samtools-0.1.1/bam_import.c:119: undefined reference to > `gzclose' > /home/stine/samtools-0.1.1/bam_import.c:103: undefined reference to > `gzopen64' > ./libbam.a(bam_import.o): In function `sam_open': > /home/stine/samtools-0.1.1/bam_import.c:320: undefined reference to > `gzdopen' > /home/stine/samtools-0.1.1/bam_import.c:320: undefined reference to > `gzopen64' > ./libbam.a(bam_import.o): In function `sam_close': > /home/stine/samtools-0.1.1/bam_import.c:330: undefined reference to > `gzclose' > ./libbam.a(bgzf.o): In function `deflate_block': > /home/stine/samtools-0.1.1/bgzf.c:206: undefined reference to `deflate' > /home/stine/samtools-0.1.1/bgzf.c:208: undefined reference to `deflateEnd' > /home/stine/samtools-0.1.1/bgzf.c:200: undefined reference to > `deflateInit2_' > /home/stine/samtools-0.1.1/bgzf.c:224: undefined reference to `deflateEnd' > /home/stine/samtools-0.1.1/bgzf.c:240: undefined reference to `crc32' > /home/stine/samtools-0.1.1/bgzf.c:241: undefined reference to `crc32' > ./libbam.a(bgzf.o): In function `inflate_block': > /home/stine/samtools-0.1.1/bgzf.c:274: undefined reference to > `inflateInit2_' > /home/stine/samtools-0.1.1/bgzf.c:279: undefined reference to `inflate' > /home/stine/samtools-0.1.1/bgzf.c:285: undefined reference to `inflateEnd' > ./libbam.a(bgzf.o): In function `read_block': > /home/stine/samtools-0.1.1/bgzf.c:281: undefined reference to `inflateEnd' > ./libbam.a(bam_maqcns.o): In function `cal_coef': > /home/stine/samtools-0.1.1/bam_maqcns.c:68: undefined reference to `pow' > /home/stine/samtools-0.1.1/bam_maqcns.c:73: undefined reference to `lgamma' > /home/stine/samtools-0.1.1/bam_maqcns.c:73: undefined reference to `lgamma' > /home/stine/samtools-0.1.1/bam_maqcns.c:73: undefined reference to `lgamma' > /home/stine/samtools-0.1.1/bam_maqcns.c:75: undefined reference to `pow' > /home/stine/samtools-0.1.1/bam_maqcns.c:76: undefined reference to `log' > /home/stine/samtools-0.1.1/bam_maqcns.c:77: undefined reference to `log' > /home/stine/samtools-0.1.1/bam_maqcns.c:82: undefined reference to `expl' > /home/stine/samtools-0.1.1/bam_maqcns.c:87: undefined reference to `logl' > /home/stine/samtools-0.1.1/bam_maqcns.c:90: undefined reference to `logl' > /home/stine/samtools-0.1.1/bam_maqcns.c:90: undefined reference to `expl' > /home/stine/samtools-0.1.1/bam_maqcns.c:90: undefined reference to `logl' > /home/stine/samtools-0.1.1/bam_maqcns.c:90: undefined reference to `logl' > /home/stine/samtools-0.1.1/bam_maqcns.c:90: undefined reference to `expl' > /home/stine/samtools-0.1.1/bam_maqcns.c:90: undefined reference to `logl' > ./libbam.a(bam_maqcns.o): In function `cal_het': > /home/stine/samtools-0.1.1/bam_maqcns.c:38: undefined reference to `lgamma' > /home/stine/samtools-0.1.1/bam_maqcns.c:38: undefined reference to `lgamma' > /home/stine/samtools-0.1.1/bam_maqcns.c:38: undefined reference to `lgamma' > /home/stine/samtools-0.1.1/bam_maqcns.c:41: undefined reference to `log' > /home/stine/samtools-0.1.1/bam_maqcns.c:42: undefined reference to `log' > /home/stine/samtools-0.1.1/bam_maqcns.c:43: undefined reference to `expl' > /home/stine/samtools-0.1.1/bam_maqcns.c:43: undefined reference to `expl' > /home/stine/samtools-0.1.1/bam_maqcns.c:43: undefined reference to `expl' > /home/stine/samtools-0.1.1/bam_maqcns.c:43: undefined reference to `expl' > /home/stine/samtools-0.1.1/bam_maqcns.c:45: undefined reference to `logl' > /home/stine/samtools-0.1.1/bam_maqcns.c:51: undefined reference to `log' > ./libbam.a(razf.o): In function `_razf_write': > /home/stine/samtools-0.1.1/razf.c:140: undefined reference to `deflate' > ./libbam.a(razf.o): In function `razf_open_w': > /home/stine/samtools-0.1.1/razf.c:113: undefined reference to > `deflateInit2_' > /home/stine/samtools-0.1.1/razf.c:129: undefined reference to > `deflateSetHeader' > ./libbam.a(razf.o): In function `razf_open_r': > /home/stine/samtools-0.1.1/razf.c:300: undefined reference to > `inflateInit2_' > /home/stine/samtools-0.1.1/razf.c:301: undefined reference to `inflateEnd' > ./libbam.a(razf.o): In function `_razf_read': > /home/stine/samtools-0.1.1/razf.c:433: undefined reference to `inflate' > ./libbam.a(razf.o): In function `razf_flush': > /home/stine/samtools-0.1.1/razf.c:165: undefined reference to `deflate' > ./libbam.a(razf.o): In function `_razf_reset_read': > /home/stine/samtools-0.1.1/razf.c:536: undefined reference to > `inflateReset' > /home/stine/samtools-0.1.1/razf.c:536: undefined reference to > `inflateReset' > ./libbam.a(razf.o): In function `razf_close': > /home/stine/samtools-0.1.1/razf.c:629: undefined reference to `inflateEnd' > ./libbam.a(razf.o): In function `razf_end_flush': > /home/stine/samtools-0.1.1/razf.c:185: undefined reference to `deflate' > ./libbam.a(razf.o): In function `razf_close': > /home/stine/samtools-0.1.1/razf.c:617: undefined reference to `deflateEnd' > collect2: error: ld returned 1 exit status > make[1]: *** [samtools] Error 1 > make[1]: Leaving directory `/home/stine/samtools-0.1.1' > make: *** [all-recur] Error 1 > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > >
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