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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.
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
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
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