Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • tmap aligner install problem

    Hi All,

    I trying to use the Ubuntu_16.04.3_TLS server to install the tmap aliger but I suffering on some problem.
    I saw a lot of people say Ubuntu need to install 18 application before install the tmap but one of the software 'liblapack3gf ' I can not find it.
    However I still try to install the tmap but it pump up a lot of undefined reference error.
    Can someone let me know how to fix it?
    Thanks.

    Tha following text are part of the error massage.
    gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/tmap_main.o -MD -MP -MF $depbase.Tpo -c -o src/tmap_main.o src/tmap_main.c &&\
    mv -f $depbase.Tpo $depbase.Po
    In file included from src/tmap_main.c:12:0:
    src/util/tmap_definitions.h:361:1: warning: inline function ‘tmap_interval_overlap’ declared but never defined
    tmap_interval_overlap(uint32_t low1, uint32_t high1, uint32_t low2, uint32_t high2);
    ^
    src/util/tmap_definitions.h:342:1: warning: inline function ‘tmap_to_char’ declared but never defined
    tmap_to_char(char *seq, int32_t len);
    ^
    src/util/tmap_definitions.h:334:1: warning: inline function ‘tmap_to_int’ declared but never defined
    tmap_to_int(char *seq, int32_t len);
    ^
    src/util/tmap_definitions.h:326:1: warning: inline function ‘tmap_compliment’ declared but never defined
    tmap_compliment(char *seq, int32_t len);
    ^
    src/util/tmap_definitions.h:318:1: warning: inline function ‘tmap_reverse_compliment_int’ declared but never defined
    tmap_reverse_compliment_int(uint8_t *seq, int32_t len);
    ^
    src/util/tmap_definitions.h:310:1: warning: inline function ‘tmap_reverse_compliment’ declared but never defined
    tmap_reverse_compliment(char *seq, int32_t len);
    ^
    src/util/tmap_definitions.h:302:1: warning: inline function ‘tmap_reverse_int’ declared but never defined
    tmap_reverse_int(uint8_t *seq, int32_t len);
    ^
    src/util/tmap_definitions.h:294:1: warning: inline function ‘tmap_reverse’ declared but never defined
    tmap_reverse(char *seq, int32_t len);
    ^
    src/util/tmap_definitions.h:262:1: warning: inline function ‘tmap_get_file_name’ declared but never defined
    tmap_get_file_name(const char *prefix, int32_t type);
    ^
    src/util/tmap_definitions.h:253:1: warning: inline function ‘tmap_log2’ declared but never defined
    tmap_log2(uint32_t v);
    ^
    g++ -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -Isrc/samtools -o tmap src/util/tmap_alloc.o src/util/tmap_definitions.o src/util/tmap_error.o src/util/tmap_rand.o src/util/tmap_time.o src/util/tmap_fibheap.o src/util/tmap_progress.o src/util/tmap_string.o src/util/tmap_levenshtein.o src/util/tmap_sam_convert.o src/seq/tmap_fq.o src/seq/tmap_sff.o src/seq/tmap_sam.o src/seq/tmap_seq.o src/seq/tmap_seqs.o src/io/tmap_file.o src/io/tmap_fq_io.o src/io/tmap_sff_io.o src/io/tmap_sam_io.o src/io/tmap_seq_io.o src/io/tmap_seqs_io.o src/index/tmap_bwt.o src/index/tmap_bwt_aux.o src/index/tmap_bwtl.o src/index/tmap_bwt_gen.o src/index/tmap_bwt_match.o src/index/tmap_bwt_match_hash.o src/index/tmap_bwt_smem.o src/index/tmap_index.o src/index/tmap_refseq.o src/index/tmap_sa.o src/index/tmap_sa_aux.o src/index/tmap_index_size.o src/sw/tmap_sw.o src/sw/tmap_fsw.o src/sw/tmap_vsw_definitions.o src/sw/tmap_vsw.o src/sw/lib/vsw.o src/sw/lib/vsw16.o src/sw/lib/sw-vector.o src/sw/lib/Solution.o src/sw/lib/Solution1.o src/sw/lib/Solution2.o src/sw/lib/Solution3.o src/sw/lib/Solution4.o src/sw/lib/Solution5.o src/sw/lib/Solution6.o src/sw/lib/Solution7.o src/sw/lib/Solution8.o src/sw/lib/Solution9.o src/sw/lib/Solution10.o src/sw/lib/AffineSWOptimization.o src/sw/lib/AffineSWOptimizationHash.o src/sw/lib/AffineSWOptimizationWrapper.o src/sw/tmap_vsw_bm.o src/samtools/bam.o src/samtools/sam.o src/samtools/sam_header.o src/samtools/bam_import.o src/samtools/bam_aux.o src/samtools/bam_pileup.o src/samtools/bam_lpileup.o src/samtools/bam_md.o src/samtools/faidx.o src/samtools/bedidx.o src/samtools/razf.o src/samtools/bgzf.o src/samtools/kstring.o src/samtools/knetfile.o src/samtools/kaln.o src/samtools/kprobaln.o src/samtools/bam_index.o src/samtools/bam_sort.o src/samtools/bam_reheader.o src/samtools/bam_cat.o src/samtools/bam_tview.o src/samtools/bam_plcmd.o src/samtools/sam_view.o src/samtools/bam_rmdup.o src/samtools/bam_rmdupse.o src/samtools/bam_mate.o src/samtools/bam_stat.o src/samtools/bam_color.o src/samtools/bam2bcf.o src/samtools/bam2bcf_indel.o src/samtools/errmod.o src/samtools/sample.o src/samtools/cut_target.o src/samtools/phase.o src/samtools/bam2depth.o src/samtools/padding.o src/samtools/bcftools/bcf.o src/samtools/bcftools/bcf2qcall.o src/samtools/bcftools/bcfutils.o src/samtools/bcftools/call1.o src/samtools/bcftools/em.o src/samtools/bcftools/fet.o src/samtools/bcftools/index.o src/samtools/bcftools/kfunc.o src/samtools/bcftools/kmin.o src/samtools/bcftools/main.o src/samtools/bcftools/mut.o src/samtools/bcftools/prob1.o src/samtools/bcftools/vcf.o src/samtools/bamtk.o src/server/tmap_server.o src/server/tmap_shm.o src/sam2fs/tmap_sam2fs_aux.o src/sam2fs/tmap_sam2fs.o src/index/tmap_index_speed.o src/index/tmap_bwt_check.o src/index/tmap_bwt_compare.o src/map/util/tmap_map_opt.o src/map/util/tmap_map_stats.o src/map/util/tmap_map_util.o src/map/pairing/tmap_map_pairing.o src/map/map1/tmap_map1.o src/map/map1/tmap_map1_aux.o src/map/map2/tmap_map2.o src/map/map2/tmap_map2_aux.o src/map/map2/tmap_map2_chain.o src/map/map2/tmap_map2_core.o src/map/map2/tmap_map2_mempool.o src/map/map3/tmap_map3.o src/map/map3/tmap_map3_aux.o src/map/map4/tmap_map4.o src/map/map4/tmap_map4_aux.o src/map/mapvsw/tmap_map_vsw.o src/map/mapall/tmap_map_all.o src/map/tmap_map_driver.o src/tmap_main.o -lpthread -lm -lz -lbz2
    src/util/tmap_string.o: In function `tmap_string_reverse_compliment':
    /root/TMAP/src/util/tmap_string.c:124: undefined reference to `tmap_reverse_compliment'
    src/util/tmap_string.o: In function `tmap_string_compliment':
    /root/TMAP/src/util/tmap_string.c:140: undefined reference to `tmap_compliment'
    src/seq/tmap_fq.o: In function `tmap_fq_reverse':
    /root/TMAP/src/seq/tmap_fq.c:51: undefined reference to `tmap_string_reverse'
    /root/TMAP/src/seq/tmap_fq.c:52: undefined reference to `tmap_string_reverse'
    src/seq/tmap_fq.o: In function `tmap_fq_reverse_compliment':
    /root/TMAP/src/seq/tmap_fq.c:59: undefined reference to `tmap_string_reverse'
    src/seq/tmap_sff.o: In function `tmap_sff_header_read':
    /root/TMAP/src/seq/tmap_sff.c:85: undefined reference to `tmap_string_init'
    /root/TMAP/src/seq/tmap_sff.c:86: undefined reference to `tmap_string_init'
    src/seq/tmap_sff.o: In function `tmap_sff_header_destroy':
    /root/TMAP/src/seq/tmap_sff.c:117: undefined reference to `tmap_string_destroy'
    /root/TMAP/src/seq/tmap_sff.c:118: undefined reference to `tmap_string_destroy'
    src/seq/tmap_sff.o: In function `tmap_sff_read_header_read':
    /root/TMAP/src/seq/tmap_sff.c:173: undefined reference to `tmap_string_init'
    src/seq/tmap_sff.o: In function `tmap_sff_read_header_destroy':
    /root/TMAP/src/seq/tmap_sff.c:201: undefined reference to `tmap_string_destroy'
    .
    .
    .
    ./root/TMAP/src/map/tmap_map_driver.c:643: undefined reference to `tmap_seq_get_bases_length'
    src/map/tmap_map_driver.o:/root/TMAP/src/map/tmap_map_driver.c:643: more undefined references to `tmap_seq_get_bases_length' follow
    collect2: error: ld returned 1 exit status
    Makefile:1127: recipe for target 'tmap' failed
    make[2]: *** [tmap] Error 1
    make[2]: Leaving directory '/root/TMAP'
    Makefile:1348: recipe for target 'all-recursive' failed
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory '/root/TMAP'
    Makefile:632: recipe for target 'all' failed
    make: *** [all] Error 2

  • #2
    Hi,

    I had the same problem on my computer. After adding -fgnu89-inline to extended_CFLAGS in configure.ac file, everything was ok.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X