search

atks / vt

A tool set for short variant discovery in genetic sequence data.
http://genome.sph.umich.edu/wiki/vt
MIT License
192 stars 3 forks source link

installation problem on RHEl 5.5 #72

Closed bioinfo-dirty-jobs closed 5 years ago

bioinfo-dirty-jobs commented 7 years ago

Dear All, I need to install vt on my server RHEL 5.5 Could you please help me?

[sbsuser@compute-00-01 vt]$ make
g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -D__STDC_LIMIT_MACROS -o ahmm.o -c ahmm.cpp
cc1plus: error: unrecognized command line option "-std=c++0x"
make: *** [ahmm.o] Error 1
[sbsuser@compute-00-01 vt]$ make clean
cd lib/htslib; make clean
make[1]: Entering directory `/illumina/software/PROG2/vt/lib/htslib'
rm -f test/*.tmp test/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.so libhts.so.*
rm -f libhts.a bgzip htsfile tabix  test/hts_endian test/fieldarith test/hfile test/sam test/test_bgzf test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6
make[1]: Leaving directory `/illumina/software/PROG2/vt/lib/htslib'
cd lib/Rmath; make clean
make[1]: Entering directory `/illumina/software/PROG2/vt/lib/Rmath'
rm -f *.o *.do *.a *.a core* *~ *#
make[1]: Leaving directory `/illumina/software/PROG2/vt/lib/Rmath'
cd lib/pcre2; make clean
make[1]: Entering directory `/illumina/software/PROG2/vt/lib/pcre2'
rm *.o *.a
make[1]: Leaving directory `/illumina/software/PROG2/vt/lib/pcre2'
cd lib/libsvm; make clean
make[1]: Entering directory `/illumina/software/PROG2/vt/lib/libsvm'
rm -f *~ svm.o libsvm.so.2 libsvm.a
make[1]: Leaving directory `/illumina/software/PROG2/vt/lib/libsvm'
rm -rf vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_mendelian.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o
[sbsuser@compute-00-01 vt]$ make 
cd lib/htslib; make libhts.a || exit 1; 
make[1]: Entering directory `/illumina/software/PROG2/vt/lib/htslib'
gcc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I.  -c -o kstring.o kstring.c
kstring.c: In function ‘kputd’:
kstring.c:40: warning: implicit declaration of function ‘signbit’
gcc -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
bcf_sr_sort.c: In function ‘merge_vsets’:
bcf_sr_sort.c:228: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c: In function ‘push_vset’:
bcf_sr_sort.c:248: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c: In function ‘grp_create_key’:
bcf_sr_sort.c:304: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c: In function ‘bcf_sr_sort_set’:
bcf_sr_sort.c:359: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:403: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:417: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:423: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:431: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:463: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:467: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:489: warning: dereferencing type-punned pointer will break strict-aliasing rules
bcf_sr_sort.c:490: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.4"' > version.h
gcc -g -Wall -O2 -I.  -c -o hts.o hts.c
hts.c: In function ‘hts_parse_opt_list’:
hts.c:679: warning: dereferencing type-punned pointer will break strict-aliasing rules
hts.c: In function ‘hts_readlist’:
hts.c:1117: warning: dereferencing type-punned pointer will break strict-aliasing rules
hts.c:1131: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -I.  -c -o multipart.o multipart.c
multipart.c: In function ‘parse_ga4gh_redirect_json’:
multipart.c:164: warning: dereferencing type-punned pointer will break strict-aliasing rules
multipart.c:189: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -I.  -c -o regidx.o regidx.c
regidx.c: In function ‘regidx_insert’:
regidx.c:136: warning: dereferencing type-punned pointer will break strict-aliasing rules
regidx.c:137: warning: dereferencing type-punned pointer will break strict-aliasing rules
regidx.c:145: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
synced_bcf_reader.c: In function ‘_regions_add’:
synced_bcf_reader.c:800: warning: dereferencing type-punned pointer will break strict-aliasing rules
synced_bcf_reader.c: In function ‘_regions_match_alleles’:
synced_bcf_reader.c:1155: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
vcf_sweep.c: In function ‘sw_rec_save’:
vcf_sweep.c:79: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf_sweep.c: In function ‘sw_fill_buffer’:
vcf_sweep.c:101: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf_sweep.c: In function ‘bcf_sweep_fwd’:
vcf_sweep.c:167: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I.  -c -o vcf.o vcf.c
vcf.c: In function ‘bcf_subset_format’:
vcf.c:1199: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c: In function ‘bcf_unpack’:
vcf.c:2388: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c:2399: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c:2408: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c:2416: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c: In function ‘bcf_update_info’:
vcf.c:3257: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c: In function ‘bcf_update_format’:
vcf.c:3356: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c: In function ‘bcf_update_filter’:
vcf.c:3404: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c: In function ‘bcf_add_filter’:
vcf.c:3425: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcf.c: In function ‘_bcf1_sync_alleles’:
vcf.c:3463: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
vcfutils.c: In function ‘bcf_remove_allele_set’:
vcfutils.c:291: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcfutils.c:494: warning: dereferencing type-punned pointer will break strict-aliasing rules
vcfutils.c:543: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c:60:18: error: lzma.h: No such file or directory
cram/cram_io.c: In function ‘lzma_mem_deflate’:
cram/cram_io.c:865: warning: implicit declaration of function ‘lzma_stream_buffer_bound’
cram/cram_io.c:871: error: ‘LZMA_OK’ undeclared (first use in this function)
cram/cram_io.c:871: error: (Each undeclared identifier is reported only once
cram/cram_io.c:871: error: for each function it appears in.)
cram/cram_io.c:871: warning: implicit declaration of function ‘lzma_easy_buffer_encode’
cram/cram_io.c:871: error: ‘LZMA_CHECK_CRC32’ undeclared (first use in this function)
cram/cram_io.c: In function ‘lzma_mem_inflate’:
cram/cram_io.c:881: error: ‘lzma_stream’ undeclared (first use in this function)
cram/cram_io.c:881: error: expected ‘;’ before ‘strm’
cram/cram_io.c:887: error: ‘LZMA_OK’ undeclared (first use in this function)
cram/cram_io.c:887: warning: implicit declaration of function ‘lzma_stream_decoder’
cram/cram_io.c:887: error: ‘strm’ undeclared (first use in this function)
cram/cram_io.c:887: warning: implicit declaration of function ‘lzma_easy_decoder_memusage’
cram/cram_io.c:902: warning: implicit declaration of function ‘lzma_code’
cram/cram_io.c:902: error: ‘LZMA_RUN’ undeclared (first use in this function)
cram/cram_io.c:903: error: ‘LZMA_STREAM_END’ undeclared (first use in this function)
cram/cram_io.c:915: error: ‘LZMA_FINISH’ undeclared (first use in this function)
cram/cram_io.c:924: warning: implicit declaration of function ‘lzma_end’
make[1]: *** [cram/cram_io.o] Error 1
make[1]: Leaving directory `/illumina/software/PROG2/vt/lib/htslib'
make: *** [lib/htslib/libhts.a] Error 1
atks commented 7 years ago

@bioinfo-dirty-jobs - update your g++ to the latest version.

yuhongning commented 6 years ago

Hi, My installation error happens at this step:

svm_train.cpp: In member function 'void::Igor::inverse_normalize(std::vector<float, std::allocator >&, std::vector<float, std::allocator >&)': svm_train.cpp:165: error: no matching function for call to 'sort(gnu_cxx::__normal_iterator<float*, std::vector<float, std::allocator<float*> > >, gnu_cxx::__normal_iterator<float*, std::vector<float, std::allocator<float*> > >, ::Igor::inverse_normalize(std::vector<float, std::allocator >&, std::vector<float, std::allocator >&)::&)' make: *** [svm_train.o] Error 1

Your suggestions is highly appreciated! Yuhong

atks commented 6 years ago

@yuhongning

Hi Yuhong,

Your gcc version is old. Can you use a version that is at least version 4.8.1 and above?

yuhongning commented 6 years ago

Thanks for the suggestion, Adrian. I will upgrade gcc.

On Sat, Jan 13, 2018 at 12:13 AM, Adrian Tan notifications@github.com wrote:

@yuhongning https://github.com/yuhongning

Hi Hongning,

Your gcc version is old. Can you use a version that is at least version 4.8.1 and above?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/atks/vt/issues/72#issuecomment-357417927, or mute the thread https://github.com/notifications/unsubscribe-auth/ARrNTSiXGMJ9qvOU87oOPwZYEns96jfvks5tKGWggaJpZM4Nj3BE .