search

fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
347 stars 46 forks source link

#error This file requires compiler and library support #121

Closed Caro-Ca closed 4 years ago

Caro-Ca commented 4 years ago

Hello, I am facing this problem once I type make: 

~/SURVIVOR/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: In function ‘void translate(const char*, int, float, int, strentry&)’:
../src/vcfs/Filter_vcf.cpp:18:6: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable]
  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"
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: In function ‘void overlap_snps(std::__cxx11::string, std::__cxx11::string, int, int, int, std::__cxx11::string)’:
../src/snp_overlap/Overlap_snps.cpp:192:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = start; i <= stop; i++) {
                              ^
../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps_gwas(std::__cxx11::string, std::__cxx11::string, int, int, std::__cxx11::string)’:
../src/snp_overlap/Overlap_snps.cpp:447:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (genome.find(chr) != genome.end() && genome[chr].size() > pos) {
                                                                ^
../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snpsGWASDB(std::__cxx11::string, std::__cxx11::string, int, int, int, std::__cxx11::string)’:
../src/snp_overlap/Overlap_snps.cpp:663:80: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (genome.find(snps[i].chr) != genome.end() && genome[snps[i].chr].size() > snps[i].position) {
                                                                                ^
../src/snp_overlap/Overlap_snps.cpp: In function ‘void generate_random_regions(std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string)’:
../src/snp_overlap/Overlap_snps.cpp:767:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) {
                                                  ^
../src/snp_overlap/Overlap_snps.cpp:781:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   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: In function ‘void computeAlignment(std::vector<CigarOp>, char*, std::__cxx11::string, std::vector<std::vector<std::vector<int> > >&, std::__cxx11::string)’:
../src/simulator/Error_scanner.cpp:173:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   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: In function ‘void reprotvals(const char*)’:
../src/simulator/Eval_vcf.cpp:102:8: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable]
  float dv = 0; //"# high-quality variant pairs"
        ^
../src/simulator/Eval_vcf.cpp:103:8: warning: variable ‘dr’ set but not used [-Wunused-but-set-variable]
  float dr = 0; //"# high-quality reference pairs"
        ^
../src/simulator/Eval_vcf.cpp:104:6: warning: variable ‘gq’ set but not used [-Wunused-but-set-variable]
  int gq = 0; //"Genotype Quality"
      ^
../src/simulator/Eval_vcf.cpp:105:6: warning: variable ‘rr’ set but not used [-Wunused-but-set-variable]
  int rr = 0;
      ^
../src/simulator/Eval_vcf.cpp:106:6: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable]
  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"
In file included from /usr/include/c++/5/random:35:0,
                 from ../src/simulator/Sim_reads.h:21,
                 from ../src/simulator/Sim_reads.cpp:8:
/usr/include/c++/5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support \
  ^
src/simulator/subdir.mk:33: recipe for target 'src/simulator/Sim_reads.o' failed
make: *** [src/simulator/Sim_reads.o] Error 1

Hope you could help me out. Thank you in advance.

fritzsedlazeck commented 4 years ago

Hi, are you using a Mac or a Linux machine?

Thanks Fritz

Caro-Ca commented 4 years ago

Hi, I am using a Linux machine. Thanks for replying.

fritzsedlazeck commented 4 years ago

Hi, i think I found the problem and that was on me.. .sorry for that. Can you clone and try again? Thanks Fritz

Caro-Ca commented 4 years ago

Thank you for replying and for your help. It worked!