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Can not bulid panSVR #1

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yanhl1989 opened this issue Oct 18, 2024 · 0 comments
Open

Can not bulid panSVR #1

yanhl1989 opened this issue Oct 18, 2024 · 0 comments

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@yanhl1989
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Hi, when I bulild thish project fllowed README, I got the fllowing output whith error, please give me some advice, thank you~

sh build
rm -rf ./src/kswlib/kalloc.d ./src/kswlib/kalloc.o ./src/kswlib/ksw2_dispatch.d ./src/kswlib/ksw2_dispatch.o ./src/kswlib/ksw2_extd2_sse.d ./src/kswlib/ksw2_extd2_sse.o ./src/kswlib/ksw2_exts2_sse.d ./src/kswlib/ksw2_exts2_sse.o ./src/kswlib/ksw2_extz2_sse.d ./src/kswlib/ksw2_extz2_sse.o ./src/kswlib/ksw2_ll_sse.d ./src/kswlib/ksw2_ll_sse.o
rm -rf ./src/htslib/cram/cram_codecs.d ./src/htslib/cram/cram_codecs.o ./src/htslib/cram/cram_decode.d ./src/htslib/cram/cram_decode.o ./src/htslib/cram/cram_encode.d ./src/htslib/cram/cram_encode.o ./src/htslib/cram/cram_external.d ./src/htslib/cram/cram_external.o ./src/htslib/cram/cram_index.d ./src/htslib/cram/cram_index.o ./src/htslib/cram/cram_io.d ./src/htslib/cram/cram_io.o ./src/htslib/cram/cram_samtools.d ./src/htslib/cram/cram_samtools.o ./src/htslib/cram/cram_stats.d ./src/htslib/cram/cram_stats.o ./src/htslib/cram/files.d ./src/htslib/cram/files.o ./src/htslib/cram/mFILE.d ./src/htslib/cram/mFILE.o ./src/htslib/cram/open_trace_file.d ./src/htslib/cram/open_trace_file.o ./src/htslib/cram/pooled_alloc.d ./src/htslib/cram/pooled_alloc.o ./src/htslib/cram/rANS_static.d ./src/htslib/cram/rANS_static.o ./src/htslib/cram/sam_header.d ./src/htslib/cram/sam_header.o ./src/htslib/cram/string_alloc.d ./src/htslib/cram/string_alloc.o
rm -rf ./src/htslib/bcf_sr_sort.d ./src/htslib/bcf_sr_sort.o ./src/htslib/bgzf.d ./src/htslib/bgzf.o ./src/htslib/bgzip.d ./src/htslib/bgzip.o ./src/htslib/errmod.d ./src/htslib/errmod.o ./src/htslib/faidx.d ./src/htslib/faidx.o ./src/htslib/hfile.d ./src/htslib/hfile.o ./src/htslib/hfile_gcs.d ./src/htslib/hfile_gcs.o ./src/htslib/hfile_net.d ./src/htslib/hfile_net.o ./src/htslib/hts.d ./src/htslib/hts.o ./src/htslib/hts_os.d ./src/htslib/hts_os.o ./src/htslib/htsfile.d ./src/htslib/htsfile.o ./src/htslib/kfunc.d ./src/htslib/kfunc.o ./src/htslib/knetfile.d ./src/htslib/knetfile.o ./src/htslib/kstring.d ./src/htslib/kstring.o ./src/htslib/md5.d ./src/htslib/md5.o ./src/htslib/multipart.d ./src/htslib/multipart.o ./src/htslib/probaln.d ./src/htslib/probaln.o ./src/htslib/realn.d ./src/htslib/realn.o ./src/htslib/regidx.d ./src/htslib/regidx.o ./src/htslib/sam.d ./src/htslib/sam.o ./src/htslib/synced_bcf_reader.d ./src/htslib/synced_bcf_reader.o ./src/htslib/tabix.d ./src/htslib/tabix.o ./src/htslib/tbx.d ./src/htslib/tbx.o ./src/htslib/textutils.d ./src/htslib/textutils.o ./src/htslib/thread_pool.d ./src/htslib/thread_pool.o ./src/htslib/vcf.d ./src/htslib/vcf.o ./src/htslib/vcf_sweep.d ./src/htslib/vcf_sweep.o ./src/htslib/vcfutils.d ./src/htslib/vcfutils.o
rm -rf ./src/cpp_lib/statistics/StatsManager.d ./src/cpp_lib/statistics/StatsManager.o ./src/cpp_lib/statistics/StatsTracker.d ./src/cpp_lib/statistics/StatsTracker.o
rm -rf ./src/cpp_lib/Assembler/assembler.d ./src/cpp_lib/Assembler/assembler.o ./src/cpp_lib/Assembler/mantaAssembler.d ./src/cpp_lib/Assembler/mantaAssembler.o
rm -rf ./src/cpp_lib/cpp_utils.d ./src/cpp_lib/cpp_utils.o ./src/cpp_lib/graph.d ./src/cpp_lib/graph.o
rm -rf ./src/clib/bam_file.d ./src/clib/bam_file.o ./src/clib/binarys_qsort.d ./src/clib/binarys_qsort.o ./src/clib/kthread.d ./src/clib/kthread.o ./src/clib/utils.d ./src/clib/utils.o ./src/clib/vcf_file.d ./src/clib/vcf_file.o
rm -rf ./src/PanSVgenerateVCF/SignalAssembly.d ./src/PanSVgenerateVCF/SignalAssembly.o ./src/PanSVgenerateVCF/deBGA_index.d ./src/PanSVgenerateVCF/deBGA_index.o ./src/PanSVgenerateVCF/getSignalRead.d ./src/PanSVgenerateVCF/getSignalRead.o ./src/PanSVgenerateVCF/read_realignment.d ./src/PanSVgenerateVCF/read_realignment.o
rm -rf ./src/NovaSVgenerateVCF/ReadHandler.d ./src/NovaSVgenerateVCF/ReadHandler.o ./src/NovaSVgenerateVCF/SveHandler.d ./src/NovaSVgenerateVCF/SveHandler.o ./src/NovaSVgenerateVCF/sv_main.d ./src/NovaSVgenerateVCF/sv_main.o ./src/NovaSVgenerateVCF/sve.d ./src/NovaSVgenerateVCF/sve.o
rm -rf ./src/analysis.d ./src/analysis.o ./src/main.d ./src/main.o
rm -rf panSVR

gcc -c index_build.c -o index_build.o
gcc -c seed_ali_core.c -o seed_ali_core.o
gcc -c load_input.c -o load_input.o
gcc -c bit_operation.c -o bit_operation.o
gcc -c LandauVishkin.c -o LandauVishkin.o
gcc -c ksw.c -o ksw.o
gcc -c main.c -o main.o
gcc -g -Wall -O2 index_build.o seed_ali_core.o load_input.o bit_operation.o LandauVishkin.o ksw.o main.o -lz -lpthread -lgomp -lm -o ../deBGA
cp: cannot stat ‘./Release/panSVR’: No such file or directory

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