Problem with the Compilation
rl4940 opened this issue · 2 comments
rl4940 commented
Hi Team!
Thank you for your excellent work!
I do encounter a problem here when compiling this tool in my research of combining the Sniffles2 with CuteSV:
Thank you!
Below is the message I get from running it:
(base) (base) [renqgli02@Linux02 Debug]$ ./SURVIVOR
./SURVIVOR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./SURVIVOR)
./SURVIVOR: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./SURVIVOR)
./SURVIVOR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./SURVIVOR)
Below is the super long compilation log:
[renqgli02@Linux02 Debug]$ make
Building file: ../src/vcfs/Annotate_vcf.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Annotate_vcf.d" -MT"src/vcfs/Annotate_vcf.o" -o "src/vcfs/Annotate_vcf.o" "../src/vcfs/Annotate_vcf.cpp"
Finished building: ../src/vcfs/Annotate_vcf.cpp
Building file: ../src/vcfs/Combine_3_VCF.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Combine_3_VCF.d" -MT"src/vcfs/Combine_3_VCF.o" -o "src/vcfs/Combine_3_VCF.o" "../src/vcfs/Combine_3_VCF.cpp"
Finished building: ../src/vcfs/Combine_3_VCF.cpp
Building file: ../src/vcfs/Compoverlap_VCF.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Compoverlap_VCF.d" -MT"src/vcfs/Compoverlap_VCF.o" -o "src/vcfs/Compoverlap_VCF.o" "../src/vcfs/Compoverlap_VCF.cpp"
Finished building: ../src/vcfs/Compoverlap_VCF.cpp
Building file: ../src/vcfs/Detect_nested.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Detect_nested.d" -MT"src/vcfs/Detect_nested.o" -o "src/vcfs/Detect_nested.o" "../src/vcfs/Detect_nested.cpp"
Finished building: ../src/vcfs/Detect_nested.cpp
Building file: ../src/vcfs/Filter_vcf.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Filter_vcf.d" -MT"src/vcfs/Filter_vcf.o" -o "src/vcfs/Filter_vcf.o" "../src/vcfs/Filter_vcf.cpp"
../src/vcfs/Filter_vcf.cpp: 在函数‘void translate(const char*, int, float, int, strentry&)’中:
../src/vcfs/Filter_vcf.cpp:18:6: 警告：变量‘lumpy’被设定但未被使用 [-Wunused-but-set-variable]
18 | int lumpy = 0;
| ^~~~~
Finished building: ../src/vcfs/Filter_vcf.cpp
Building file: ../src/vcfs/Generate_distMat.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Generate_distMat.d" -MT"src/vcfs/Generate_distMat.o" -o "src/vcfs/Generate_distMat.o" "../src/vcfs/Generate_distMat.cpp"
Finished building: ../src/vcfs/Generate_distMat.cpp
Building file: ../src/vcfs/Merge_VCF.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Merge_VCF.d" -MT"src/vcfs/Merge_VCF.o" -o "src/vcfs/Merge_VCF.o" "../src/vcfs/Merge_VCF.cpp"
../src/vcfs/Merge_VCF.cpp: 在函数‘strvcfentry parse_vcf_entry(std::string)’中:
../src/vcfs/Merge_VCF.cpp:379:9: 警告：变量‘freq’被设定但未被使用 [-Wunused-but-set-variable]
379 | float freq = 0;
| ^~~~
Finished building: ../src/vcfs/Merge_VCF.cpp
Building file: ../src/snp_overlap/Overlap_snps.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/snp_overlap/Overlap_snps.d" -MT"src/snp_overlap/Overlap_snps.o" -o "src/snp_overlap/Overlap_snps.o" "../src/snp_overlap/Overlap_snps.cpp"
../src/snp_overlap/Overlap_snps.cpp: 在函数‘void overlap_snps(std::string, std::string, int, int, int, std::string)’中:
../src/snp_overlap/Overlap_snps.cpp:192:30: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
192 | for (size_t i = start; i <= stop; i++) {
| ~~^~~~~~~
../src/snp_overlap/Overlap_snps.cpp: 在函数‘void overlap_snps_gwas(std::string, std::string, int, int, std::string)’中:
../src/snp_overlap/Overlap_snps.cpp:447:64: 警告：comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
447 | if (genome.find(chr) != genome.end() && genome[chr].size() > pos) {
| ~~~~~~~~~~~~~~~~~~~^~~~~
../src/snp_overlap/Overlap_snps.cpp: 在函数‘void overlap_snpsGWASDB(std::string, std::string, int, int, int, std::string)’中:
../src/snp_overlap/Overlap_snps.cpp:663:80: 警告：comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
663 | if (genome.find(snps[i].chr) != genome.end() && genome[snps[i].chr].size() > snps[i].position) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
../src/snp_overlap/Overlap_snps.cpp: 在函数‘void generate_random_regions(std::string, std::string, int, std::string)’中:
../src/snp_overlap/Overlap_snps.cpp:767:50: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
767 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~
../src/snp_overlap/Overlap_snps.cpp:781:47: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
781 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~
Finished building: ../src/snp_overlap/Overlap_snps.cpp
Building file: ../src/simulator/Error_scanner.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Error_scanner.d" -MT"src/simulator/Error_scanner.o" -o "src/simulator/Error_scanner.o" "../src/simulator/Error_scanner.cpp"
../src/simulator/Error_scanner.cpp: 在函数‘void computeAlignment(std::vector<CigarOp>, char*, std::string, std::vector<std::vector<std::vector<int> > >&, std::string)’中:
../src/simulator/Error_scanner.cpp:173:18: 警告：comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<int> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
173 | while (pos + 1 > error_mat.size()) {
| ~~~~~~~~^~~~~~~~~~~~~~~~~~
Finished building: ../src/simulator/Error_scanner.cpp
Building file: ../src/simulator/Eval_vcf.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Eval_vcf.d" -MT"src/simulator/Eval_vcf.o" -o "src/simulator/Eval_vcf.o" "../src/simulator/Eval_vcf.cpp"
../src/simulator/Eval_vcf.cpp: 在函数‘void reprotvals(const char*)’中:
../src/simulator/Eval_vcf.cpp:102:8: 警告：变量‘dv’被设定但未被使用 [-Wunused-but-set-variable]
102 | float dv = 0; //"# high-quality variant pairs"
| ^~
../src/simulator/Eval_vcf.cpp:103:8: 警告：变量‘dr’被设定但未被使用 [-Wunused-but-set-variable]
103 | float dr = 0; //"# high-quality reference pairs"
| ^~
../src/simulator/Eval_vcf.cpp:104:6: 警告：变量‘gq’被设定但未被使用 [-Wunused-but-set-variable]
104 | int gq = 0; //"Genotype Quality"
| ^~
../src/simulator/Eval_vcf.cpp:105:6: 警告：变量‘rr’被设定但未被使用 [-Wunused-but-set-variable]
105 | int rr = 0;
| ^~
../src/simulator/Eval_vcf.cpp:106:6: 警告：变量‘rv’被设定但未被使用 [-Wunused-but-set-variable]
106 | int rv = 0;
| ^~
Finished building: ../src/simulator/Eval_vcf.cpp
Building file: ../src/simulator/Pac_Simulator.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Pac_Simulator.d" -MT"src/simulator/Pac_Simulator.o" -o "src/simulator/Pac_Simulator.o" "../src/simulator/Pac_Simulator.cpp"
Finished building: ../src/simulator/Pac_Simulator.cpp
Building file: ../src/simulator/SV_Simulator.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/SV_Simulator.d" -MT"src/simulator/SV_Simulator.o" -o "src/simulator/SV_Simulator.o" "../src/simulator/SV_Simulator.cpp"
Finished building: ../src/simulator/SV_Simulator.cpp
Building file: ../src/simulator/Sim_reads.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Sim_reads.d" -MT"src/simulator/Sim_reads.o" -o "src/simulator/Sim_reads.o" "../src/simulator/Sim_reads.cpp"
Finished building: ../src/simulator/Sim_reads.cpp
Building file: ../src/simulator/test_cov.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/test_cov.d" -MT"src/simulator/test_cov.o" -o "src/simulator/test_cov.o" "../src/simulator/test_cov.cpp"
Finished building: ../src/simulator/test_cov.cpp
Building file: ../src/merge_vcf/IntervallTree.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/IntervallTree.d" -MT"src/merge_vcf/IntervallTree.o" -o "src/merge_vcf/IntervallTree.o" "../src/merge_vcf/IntervallTree.cpp"
Finished building: ../src/merge_vcf/IntervallTree.cpp
Building file: ../src/merge_vcf/combine_svs.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/combine_svs.d" -MT"src/merge_vcf/combine_svs.o" -o "src/merge_vcf/combine_svs.o" "../src/merge_vcf/combine_svs.cpp"
../src/merge_vcf/combine_svs.cpp: 在函数‘void print_entry_overlap_BND(FILE*&, SVS_Node*, int)’中:
../src/merge_vcf/combine_svs.cpp:234:24: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
234 | for (size_t i = 0; i < Parameter::Instance()->max_caller; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp:236:12: 警告：comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Support_Node*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
236 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp:236:45: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
236 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp: 在函数‘void print_entry_overlap(FILE*&, SVS_Node*, int)’中:
../src/merge_vcf/combine_svs.cpp:348:23: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
348 | for (size_t i = 0; i < Parameter::Instance()->max_caller; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp:350:11: 警告：comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Support_Node*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
350 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp:350:44: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
350 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp: 在函数‘void combine_calls_svs(std::string, int, int, int, int, int, int, std::string)’中:
../src/merge_vcf/combine_svs.cpp:541:10: 警告：变量‘type’被设定但未被使用 [-Wunused-but-set-variable]
541 | short type = (*i)->type;
| ^~~~
Finished building: ../src/merge_vcf/combine_svs.cpp
Building file: ../src/convert/ConvertMQ0Bed.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/ConvertMQ0Bed.d" -MT"src/convert/ConvertMQ0Bed.o" -o "src/convert/ConvertMQ0Bed.o" "../src/convert/ConvertMQ0Bed.cpp"
Finished building: ../src/convert/ConvertMQ0Bed.cpp
Building file: ../src/convert/Convert_Assemblytics.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Assemblytics.d" -MT"src/convert/Convert_Assemblytics.o" -o "src/convert/Convert_Assemblytics.o" "../src/convert/Convert_Assemblytics.cpp"
Finished building: ../src/convert/Convert_Assemblytics.cpp
Building file: ../src/convert/Convert_Bionano.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Bionano.d" -MT"src/convert/Convert_Bionano.o" -o "src/convert/Convert_Bionano.o" "../src/convert/Convert_Bionano.cpp"
Finished building: ../src/convert/Convert_Bionano.cpp
Building file: ../src/convert/Convert_Honey_tails.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Honey_tails.d" -MT"src/convert/Convert_Honey_tails.o" -o "src/convert/Convert_Honey_tails.o" "../src/convert/Convert_Honey_tails.cpp"
../src/convert/Convert_Honey_tails.cpp: 在函数‘void parse_honey_tails(std::string, int, std::vector<strvcfentry>&)’中:
../src/convert/Convert_Honey_tails.cpp:45:7: 警告：变量‘dist’被设定但未被使用 [-Wunused-but-set-variable]
45 | int dist=0;
| ^~~~
Finished building: ../src/convert/Convert_Honey_tails.cpp
Building file: ../src/convert/Convert_MUMmer.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_MUMmer.d" -MT"src/convert/Convert_MUMmer.o" -o "src/convert/Convert_MUMmer.o" "../src/convert/Convert_MUMmer.cpp"
Finished building: ../src/convert/Convert_MUMmer.cpp
Building file: ../src/convert/Convert_Pindel.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Pindel.d" -MT"src/convert/Convert_Pindel.o" -o "src/convert/Convert_Pindel.o" "../src/convert/Convert_Pindel.cpp"
Finished building: ../src/convert/Convert_Pindel.cpp
Building file: ../src/convert/Convert_VCF_to_BED.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_VCF_to_BED.d" -MT"src/convert/Convert_VCF_to_BED.o" -o "src/convert/Convert_VCF_to_BED.o" "../src/convert/Convert_VCF_to_BED.cpp"
Finished building: ../src/convert/Convert_VCF_to_BED.cpp
Building file: ../src/convert/Convert_hapcut2.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_hapcut2.d" -MT"src/convert/Convert_hapcut2.o" -o "src/convert/Convert_hapcut2.o" "../src/convert/Convert_hapcut2.cpp"
Finished building: ../src/convert/Convert_hapcut2.cpp
Building file: ../src/convert/Process_Coverage.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Coverage.d" -MT"src/convert/Process_Coverage.o" -o "src/convert/Process_Coverage.o" "../src/convert/Process_Coverage.cpp"
Finished building: ../src/convert/Process_Coverage.cpp
Building file: ../src/convert/Process_Lumpy.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Lumpy.d" -MT"src/convert/Process_Lumpy.o" -o "src/convert/Process_Lumpy.o" "../src/convert/Process_Lumpy.cpp"
Finished building: ../src/convert/Process_Lumpy.cpp
Building file: ../src/analysis_sv/GIAB_summary.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/GIAB_summary.d" -MT"src/analysis_sv/GIAB_summary.o" -o "src/analysis_sv/GIAB_summary.o" "../src/analysis_sv/GIAB_summary.cpp"
Finished building: ../src/analysis_sv/GIAB_summary.cpp
Building file: ../src/analysis_sv/MT_identifier.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MT_identifier.d" -MT"src/analysis_sv/MT_identifier.o" -o "src/analysis_sv/MT_identifier.o" "../src/analysis_sv/MT_identifier.cpp"
../src/analysis_sv/MT_identifier.cpp: 在函数‘int parse_read_start(std::string, bool)’中:
../src/analysis_sv/MT_identifier.cpp:13:10: 警告：unused variable ‘found’ [-Wunused-variable]
13 | size_t found = cigar.find_first_of("S");
| ^~~~~
../src/analysis_sv/MT_identifier.cpp:10:25: 警告：unused variable ‘sz’ [-Wunused-variable]
10 | std::string::size_type sz; // alias of size_t
| ^~
../src/analysis_sv/MT_identifier.cpp: 在函数‘void detect_MT_copies(std::string)’中:
../src/analysis_sv/MT_identifier.cpp:90:29: 警告：unused variable ‘sz’ [-Wunused-variable]
90 | std::string::size_type sz; // alias of size_t
| ^~
Finished building: ../src/analysis_sv/MT_identifier.cpp
Building file: ../src/analysis_sv/MUMmer_overlap.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MUMmer_overlap.d" -MT"src/analysis_sv/MUMmer_overlap.o" -o "src/analysis_sv/MUMmer_overlap.o" "../src/analysis_sv/MUMmer_overlap.cpp"
../src/analysis_sv/MUMmer_overlap.cpp: 在函数‘void comp_entries_mummer(std::vector<strvcfentry>&, std::string, int)’中:
../src/analysis_sv/MUMmer_overlap.cpp:60:7: 警告：变量‘stop’被设定但未被使用 [-Wunused-but-set-variable]
60 | int stop = 0;
| ^~~~
../src/analysis_sv/MUMmer_overlap.cpp:61:7: 警告：变量‘len’被设定但未被使用 [-Wunused-but-set-variable]
61 | int len = 0;
| ^~~
Finished building: ../src/analysis_sv/MUMmer_overlap.cpp
Building file: ../src/analysis_sv/Select_samples.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Select_samples.d" -MT"src/analysis_sv/Select_samples.o" -o "src/analysis_sv/Select_samples.o" "../src/analysis_sv/Select_samples.cpp"
Finished building: ../src/analysis_sv/Select_samples.cpp
Building file: ../src/analysis_sv/Simplify_SVs.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Simplify_SVs.d" -MT"src/analysis_sv/Simplify_SVs.o" -o "src/analysis_sv/Simplify_SVs.o" "../src/analysis_sv/Simplify_SVs.cpp"
../src/analysis_sv/Simplify_SVs.cpp: 在函数‘sv_simple_str parse_line_sv(char*, int, std::vector<std::__cxx11::basic_string<char> >, std::string&)’中:
../src/analysis_sv/Simplify_SVs.cpp:54:23: 警告：comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) {
| ~~^~~~~~~~~~~~~
../src/analysis_sv/Simplify_SVs.cpp: 在函数‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >)’中:
../src/analysis_sv/Simplify_SVs.cpp:118:17: 警告：comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
118 | if (count + 1 < entry.accessions.size()) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
Finished building: ../src/analysis_sv/Simplify_SVs.cpp
Building file: ../src/analysis_sv/Summ_mat.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Summ_mat.d" -MT"src/analysis_sv/Summ_mat.o" -o "src/analysis_sv/Summ_mat.o" "../src/analysis_sv/Summ_mat.cpp"
Finished building: ../src/analysis_sv/Summ_mat.cpp
Building file: ../src/CorrectAllele.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/CorrectAllele.d" -MT"src/CorrectAllele.o" -o "src/CorrectAllele.o" "../src/CorrectAllele.cpp"
Finished building: ../src/CorrectAllele.cpp
Building file: ../src/DetectDif.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/DetectDif.d" -MT"src/DetectDif.o" -o "src/DetectDif.o" "../src/DetectDif.cpp"
Finished building: ../src/DetectDif.cpp
Building file: ../src/Extract_Seq.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Extract_Seq.d" -MT"src/Extract_Seq.o" -o "src/Extract_Seq.o" "../src/Extract_Seq.cpp"
Finished building: ../src/Extract_Seq.cpp
Building file: ../src/SURVIVOR.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/SURVIVOR.d" -MT"src/SURVIVOR.o" -o "src/SURVIVOR.o" "../src/SURVIVOR.cpp"
Finished building: ../src/SURVIVOR.cpp
Building file: ../src/Summarize_SV.cpp
Invoking: Cross G++ Compiler
g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Summarize_SV.d" -MT"src/Summarize_SV.o" -o "src/Summarize_SV.o" "../src/Summarize_SV.cpp"
../src/Summarize_SV.cpp: 在函数‘void summary_SV_stream(int, int, std::string)’中:
../src/Summarize_SV.cpp:302:42: 警告：此函数中的‘type’在使用前可能未初始化 [-Wmaybe-uninitialized]
302 | if (max_size < 0 || (leng < max_size || type == 3)) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
rl4940 commented
I am using CentOS7 as my system
rl4940 commented
It's the problem on my side, the libC++ has something went wrong